National Park Service 

U.S. Department of the Interior 

Natural Resources Program Center 

Large Rivers Water Quality Monitoring Protocol 

Great Lakes Inventory and Monitoring Network 

Natural Resource Report NPS/GLKN/NRR—2008/060 
ON THE COVER 

Top: Barge traffic on the Mississippi River in Mississippi National River and Recreation Area. Photograph by Jennifer Sieracki. 

Bottom: Namekagon River, in the St. Croix National Scenic Riverway. Photograph by David VanderMeulen
Large Rivers Water Quality Monitoring Protocol 

Great Lakes Inventory and Monitoring Network 

Version 1.0 

National Park Service 

Great Lakes Inventory and Monitoring Network 

Prepared by 

Suzanne Magdalene and Daniel Engstrom 

St. Croix Watershed Research Station 

16910 152nd. St. North 

Marine on St. Croix, Minnesota 55047 

and 

Joan Elias (contact author) 

National Park Service 

Great Lakes Inventory and Monitoring Network 

2800 Lake Shore Drive East 

Ashland, Wisconsin 54806 

joan_elias@nps.gov 

August 2008 

U.S. Department of the Interior 

National Park Service 

Natural Resource Program Center 

Fort Collins, Colorado 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

ii

The Natural Resource Publication series addresses natural resource topics that are of interest and 

applicability to a broad readership in the National Park Service and to others in the management 

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general, diverse audience, and may contain NPS policy considerations or address sensitive issues 

of management applicability. Examples of the diverse array of reports published in this series 

include vital signs monitoring plans; monitoring protocols; "how to" resource management 

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resource programs or divisions of the Natural Resource Program Center; resource action plans; 

fact sheets; and regularly-published newsletters. 

Views, statements, findings, conclusions, recommendations and data in this report are solely 

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Printed copies of reports in these series may be produced in a limited quantity and they are only 

available as long as the supply lasts. This report is also available from the Natural Resource 

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Internet, or by sending a request to the address on the back cover. 

Please cite this publication as: 

Magdalene S., D.R. Engstrom, and J. Elias. 2008. Large rivers water quality monitoring protocol, 

Version 1.0. National Park Service, Great Lakes Network, Ashland, Wisconsin. 

NPS/GLKN/NRR—2008/060. National Park Service, Fort Collins, Colorado.

 

NPS D-82, August 2008 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

iii

Contents

Page 

Tables...............................................................................................................................................v 

Figures........................................................................................................................................... vii 

Standard Operating Procedures...................................................................................................... ix 

Revision History Log.......................................................................................................................x 

Acknowledgements........................................................................................................................ xi 

List of Abbreviations .................................................................................................................... xii 

1.0 Background and Objectives .................................................................................................1 

 1.1 Rationale for Selecting this Resource to Monitor..........................................................1 

1.2 Background and History; Description of Resource .......................................................3 

1.3 Measurable Objectives.................................................................................................10 

1.4 Quality Assurance and Quality Control.......................................................................11 

2.0 Sampling Design................................................................................................................13 

 2.1 Rationale for Selecting this Sampling Design Over Others.........................................13 

 2.2 Site-Selection ...............................................................................................................18 

 2.3 Historical Variability and Statistical Power Analysis..................................................19 

 2.4 Number and Location of Monitoring Stations.............................................................23 

 2.5 Frequency and Timing of Sampling ............................................................................30 

 2.6 Level of Change that can be Detected by Proposed Sampling Design........................32 

 2.7 Expectation of Improvement in Post-hoc Statistical Power ........................................33 

3.0 Sampling Methods .............................................................................................................35 

 3.1 Field Season Preparations............................................................................................35 

 3.2 Details of Taking Field Measurements and Collecting Samples.................................37 

 3.3 Post-Collection Sample Processing. ............................................................................42 

 3.4 End of Field Season Procedures ..................................................................................43 

 3.5 Quality Assurance and Quality Control Pertaining to Sampling Methods..................43 

4.0 Data Handling, Analysis, and Reporting ...........................................................................49 

 4.1 Metadata Procedures....................................................................................................49 

 4.2 Overview of Database Design .....................................................................................49 

 4.3 Data Entry, Verification, and Editing ..........................................................................50 

 4.4 Data Archival Procedures ............................................................................................50 

 4.5 Quality Assurance and Quality Control Pertaining to Data Management...................51 

 4.6 Routine Data Summaries .............................................................................................51 

 4.7 Methods for Long-Term Trend Analysis.....................................................................52 

 4.8 Reporting Schedule......................................................................................................53 

 4.9 Report Format ..............................................................................................................54 

5.0 Personnel Requirements and Training...............................................................................57 

 5.1 Roles and Responsibilities ...........................................................................................57 

 5.2 Crew Qualifications .....................................................................................................59

 5.3 Training Procedures.....................................................................................................59 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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Contents (continued)

Page 

6.0 Operational Requirements .................................................................................................61

 6.1 Annual Workload and Field Schedule .........................................................................61 

 6.2 Facility and Equipment Needs.....................................................................................61 

 6.3 Startup Costs and Budget Considerations....................................................................61 

 6.4 Procedures for Revising and Archiving Previous Versions of the Protocol................65 

7.0 Literature Cited ..................................................................................................................67 

 Standard Operating Procedures..........................................................................................73 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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Tables 

Page 

Table 1. Historical water quality monitoring stations located within or near MISS. ..................4 

Table 2. Water quality variables and locations of Minnesota 303(d) listings within MISS........6 

Table 3. Historical water quality monitoring stations located within or near SACN. .................8 

Table 4. Water quality variables and location of Minnesota and Wisconsin 303(d) listings 

 within SACN................................................................................................................10 

Table 5. The statistical power of SACN historical monitoring efforts to detect change ...........21 

Table 6. The statistical power of MISS historical monitoring efforts to detect change ............22 

Table 7. Two-sample comparisons of MISS historical water quality data ................................23 

Table 8. The predicted sample size required to detect a 20% change at 80% power in the 

 Upper and Lower St. Croix..........................................................................................25 

Table 9. The predicted sample required to detect a 20% change at 80% power in MISS.........28 

Table 10. Number of randomly- and nonrandomly-selected monitoring stations in Upper 

 SACN, Lower SACN, and MISS.................................................................................29 

Table 11. Sampling frequency sensitivity analysis......................................................................31 

Table 12. Panel array of sampling frequency and return period..................................................31 

Table 13. Minimum detectable change for proposed sampling design within SACN.................32 

Table 14. Number of years required to detect 20% change at 80% power within SACN............34 

Table 15. Checklists of equipment and supplies..........................................................................35 

Table 16. Checklist of preparation for field season .....................................................................36 

Table 17. Typical sensor performance specifications for multiprobe field instruments..............39 

Table 18. Core suite of field variables and required methods for in situ measurements.............40 

Table 19. Example ranges of analytical methods, MDLs, containers, and holding times...........41 

Table 20. Summary of QA/QC procedures pertaining to sampling methods ..............................44 

Table 21. Ideal calibration frequencies and acceptance criteria ..................................................45 

Table 22. Summary of the types of QA/QC samples...................................................................47 

Table 23. Summary of QA/QC procedures pertaining to data management ...............................52 

Table 24. Expected start-up costs of water quality monitoring program.....................................62 

Table 25. Estimated annual costs of staff salaries and benefits...................................................63 

Table 26. Estimates of annual travel costs...................................................................................63 

Table 27. Estimates of laboratory costs for analysis of standard water quality parameters ........64 

Table 28. Estimated annual costs of laboratory analyses.............................................................65 

Table 29. Estimated total annual costs.........................................................................................65 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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Figures 

Page 

Figure 1. Map of the Mississippi River within the MISS park unit ..............................................5 

Figure 2. Map of the St. Croix and Namekagon Rivers within the upper portion of SACN ........7 

Figure 3. Map of the St. Croix River within the lower portion of SACN.....................................7 

Figure 4. Geographic distribution of environmental settings and sampling sites within a 

 NAWQA study unit .....................................................................................................14 

Figure 5. Example of a random statistical sample selection process for stream networks .........15 

Figure 6. Schematic diagram of National Park Service park unit centered on a major river......16 

Figure 7. Land cover of the St. Croix River basin ......................................................................17 

Figure 8. Screen snap-shot of on-line statistical sample size calculator .....................................20 

Figure 9. Monitoring stations within SACN ...............................................................................27 

Figure 10. Monitoring stations within MISS.................................................................................29 

Figure 11. Screen snap-shot of TRENDS statistical power analysis software..............................33 

Figure 12. Example of box-and-whisker plot................................................................................55 

Figure 13. Example of scatter plot ................................................................................................55 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

viii
ix 

Standard Operating Procedures 

SOP #1: Pre-Season Procedures 

SOP #2: Training and Safety 

SOP #3: Using a GPS 

SOP #4: Site Establishment 

SOP #5: Decontamination of Equipment to Remove Exotic Species 

SOP #6: Field Measurements and Water Sample Collection 

SOP #7: Processing Water Samples and Analytical Laboratory Requirements 

SOP #8: Data Entry and Management 

SOP #9: Data Analysis 

SOP #10: Reporting 

SOP #11: Post-Season Procedures 

SOP #12: Quality Assurance/Quality Control 

SOP #13: Revising the Protocol 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

x

Revision History Log 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project manager must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the header of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log: 

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

xi

Acknowledgements

We would like to thank Rich Axler and Elaine Ruzycki for early discussions planning for this 

protocol and for drafting several SOPs. Thanks also go to the following Great Lakes Inventory 

and Monitoring Network staff: Erik Beever for key advice on interpretation of power analyses 

and statistical design, Mark Hart for drafting the data management portion of the protocol, 

Suzanne Sanders for verbiage on reporting, Ulf Gafvert for the map of sampling locations on the 

St. Croix and Namakagon Rivers, Jennifer Sieracki for the map of sampling locations on the 

Mississippi River, and Tracey Ledder for details on quality assurance and quality control. 

 

We relied heavily on the monitoring protocols of others, especially those of the Greater 

Yellowstone Network (O’Ney 2005), EPA-EMAP (McDonald et al. 2002), and USGS (Gilliom 

et al. 1995). 

 

Finally, we would like to acknowledge the many reviewers who provided valuable comments on 

an earlier version of this protocol. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

xii

List of Abbreviations 

cfs - cubic feet per second 

EPA - Environmental Protection Agency 

EMAP - Environmental Monitoring and Assessment Program 

GLKN - Great Lakes Inventory and Monitoring Network 

MCES - Metropolitan Council Environmental Services 

mg/L - milligrams per liter 

MISS - Mississippi National River and Recreation Area 

MPCA - Minnesota Pollution Control Agency 

NAWQA - National Water Quality Assessment Program 

NPSTORET - National Park Service Storage and Retrieval Database 

SACN - St. Croix National Scenic Riverway 

STORET - Storage and Retrieval Database 

USGS - United States Geological Survey 

WDNR - Wisconsin Department of Natural Resources 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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1.0 Background and Objectives 

1.1 Rationale for Selecting this Resource to Monitor 

1.1.1 Threatened Natural Resource 

Large temperate rivers around the world have been historically affected by human activities and 

face an uncertain future in which water quality may be further threatened by climate change, 

urban development, agriculture, exotic species, recreation, and transportation uses (Meybeck and 

Helmer 1989; Zhang et al. 1999). In addition, large rivers can transfer water quality pollutants 

from land to sea, such as agricultural nitrogen in the Mississippi River causing hypoxia in the 

Gulf of Mexico (Burkart and James 1999). 

Early in the Great Lakes Network’s (hereafter, GLKN or the Network) development of a longterm monitoring plan (Route and Elias 2006), large rivers were recognized as one of the 

important ecosystems within Network parks. The National Park units in the Network that are 

based on large, non-wadeable rivers are the Mississippi National River and Recreation Area 

(MISS) and the St. Croix National Scenic Riverway (SACN). Key water quality concerns of 

these parks include: (1) excess nutrients (particularly nitrogen and phosphorus) from urban and 

agricultural runoff and wastewater treatment facilities; (2) fluctuations in flow regime caused by 

climate change, farming drainage, impervious-surfaced urban growth, or channel engineering; 

(3) sediment loading from stream-bank and agricultural-field erosion; (4) invasion of exotic 

species such as common carp (Cyprinus carpio) and zebra mussels (Dreissena polymorpha); and 

(5) environmental contaminants of emerging concern, including polybrominated diphenyl ether 

(PDBE) flame-retardants, mercury, and endocrine disrupters. 

1.1.2 Key Variables of Interest 

In scoping workshops held by the Great Lakes Network, the core suite of water quality variables 

(flow, temperature, pH, specific conductance, and dissolved oxygen) was ranked as the highest 

priority among potential vital signs (Route 2004). In addition, the advanced water quality suite 

(sediments, nutrients, ions) and water level fluctuations were ranked among the top-priority vital 

signs. A large rivers conceptual model (Lubinski 2004) identified key attributes as water flow 

and basic water quality variables, including nutrients, dissolved oxygen, sediment, and 

temperature. These variables will be the focus of the large rivers protocol. Lubinski (2004) also 

identified floodplain/channel physiography and biotic communities as important and related vital 

signs, which will be addressed under separate protocols. 

Flow is the key parameter for physical conditions in rivers; it is needed to interpret concentration 

data and calculate water quality loadings. Although part of the core water quality suite, it is 

singled out here because flow measurement is operationally different from other water quality 

monitoring. Flow regimes have been historically altered by land-use changes and may continue 

to be impacted by shifting agricultural practices, expanding urbanization, and climate change 

driven by greenhouse warming (Lenz 2004). The U.S. Geologic Survey (USGS) is the only 

agency with a program to record flow in the nation’s streams and rivers. The historical and 

ongoing data from these gaging stations are absolutely critical for the analysis of water quality 

trends and loading, and land use and climate changes. The Network has demonstrated its 

commitment to maintaining continuity of flow data records by recently contributing to the 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

2 

financial support of one of the USGS gaging stations located within SACN (on the Namekagon 

River at Leonards, Wisconsin). 

The five core water quality variables (temperature, pH, specific conductance, dissolved oxygen, 

and flow/water level) were established by a national review panel assembled by the National 

Park Service-Water Resources Division (NPS-WRD). The panel recommended this suite be 

measured across all NPS monitoring networks (Freshwater Workgroup Subcommittee 2002). In 

addition to these mandated parameters, we added measures of turbidity and clarity. Although the 

core suite was ranked highest among potential vital signs for aquatic systems of GLKN parks, it 

was recognized that these measurements were less diagnostic of water quality degradation than 

biotic communities and other water quality variables, such as nutrient concentrations. 

Excess nutrients and their effects on biological communities are among the most serious threats 

to large river systems. Expanding urbanization, agricultural intensification, encroachment of 

exotic species, and management efforts to mitigate these impacts are likely to change nutrient 

levels in these riverine parks. Nitrogen and phosphorus species will be included in this 

monitoring protocol, as well as total chlorophyll-a, which is a basic measure of phytoplankton 

biomass. 

1.1.3 Limitations of this Protocol 

The Network has a monitoring protocol for bioaccumulative contaminants, focused on bald 

eagles (Haliaeetus leucocephalus; Route et al., in preparation). An additional protocol is being 

prepared to include monitoring for mercury and organic toxic compounds in aquatic food webs 

(Wiener et al., in preparation). In addition, separate protocols for monitoring aquatic biological 

parameters (algae, macroinvertebrates, fish species, etc.) in wadeable streams and perhaps large 

rivers may be developed in the future. Therefore, the measurement variables for this large river 

water quality protocol are limited to the primarily physical and chemical parameters listed above 

in Section 1.1.2 (see complete list of monitoring parameters in Section 2.5). 

NPS-WRD has advised that newly-developed monitoring protocols include the water quality 

variables that have caused resource waters to be designated as impaired on the 303(d) list. All of 

the Mississippi River within MISS is on the 303(d) list (described in Section 1.2.1), and a portion 

of the St. Croix River within SACN is on the 303(d) list (described in Section 1.2.2). The 

Metropolitan Council Environmental Services (MCES) monitors within these two parks for 

water quality variables on the 303(d) list at the following sampling frequencies: turbidity on a 

weekly basis, and mercury and polychlorinated biphenyl (PCB) on an annual basis. The Network 

will collect blood and feathers from bald eagles for analysis of PCBs and other contaminants of 

concern, as described under a separate protocol under development (Route et al., in preparation; 

Route and Elias 2006). A portion of the blood samples will be archived, for future analysis of 

newly emerging contaminants. The Network will obtain annual water quality data updates from 

MCES to track the progress of the 303(d)-listed water quality variables, as well as data on 

bioaccumulation in bald eagles. The only 303(d)-listed water quality variable not monitored by 

MCES is fecal coliform bacteria. At this time, GLKN does not plan to monitor MISS for 

bacteria; it is unknown whether another regulatory agency is currently monitoring for bacteria 

within MISS. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

3 

1.2 Background and History; Description of Resource 

This protocol is designed to guide monitoring of the physical and chemical water quality of large 

non-wadeable rivers in park units of the Great Lakes Inventory and Monitoring Network. 

Monitoring will focus on that portion of the mainstem of the Mississippi River, which occurs 

within the Mississippi National River and Recreation Area (MISS), and the mainstems of the St. 

Croix and Namekagon Rivers, which occur in the St. Croix National Scenic Riverway (SACN). 

Neither MISS nor SACN currently has a water quality monitoring program of its own, but rather 

they rely on data collected by other agencies and institutions. The NPS-WRD retrieved data from 

several EPA databases, including STOrage and RETrieval System (STORET), and summarized 

these data for national park units (NPS 1995a, 1995b). Monitoring programs administered by 

federal, state, and regional agencies have collected data from within or near the SACN and MISS 

park boundaries since the 1920s, forming the basis for historical background information, as 

summarized in Tables 1 and 3. Monitoring sites listed in these tables are those that have been 

monitored over the long-term (at least five years) for the core suite and advanced suite variables, 

including mainstem locations and stations on major tributaries that are located within or near 

park boundaries. Many of these monitoring programs are on-going at present, and offer the 

potential for sharing data with the NPS monitoring network. By sharing data among agencies, 

sampling costs will be minimized and sampling records will be maximized. 

1.2.1 MISS – Mississippi River 

Flowing through the Twin Cities metropolitan area of Minneapolis-St. Paul, 123 km of the 

Mississippi River is included within the MISS park boundaries (Figure 1). The southern 

boundary of MISS is immediately downstream of the confluence between the Mississippi and St. 

Croix Rivers, that is, downstream of SACN. Table 1 lists locations that have been monitored by 

other government agencies for at least five years. 

Six USGS streamflow gages currently operate within or near MISS park boundaries: on the 

Mississippi River near Anoka, Minnesota (site #05288500, 1931-present) in St. Paul; Minnesota 

(site #05331000, 1892-2003) at Hastings, Minnesota (site #05331580, 1995-present) and at 

Prescott, Wisconsin (site #05344500, 1928-present); on Elm Creek near Champlin, Minnesota 

(site #05287890, 1978-present); and on Shingle Creek at Queen Avenue (site #05288705, 1996-

present). 

MISS receives heavy urban and suburban pressures, including industrial and municipal 

wastewater discharge, recreational use, and stormwater runoff. Although numerous water quality 

parameters have exceeded EPA criteria for protection of aquatic life and for drinking water in 

this stretch of the river (National Park Service 1995a), the river remains a source of drinking 

water for the Twin Cities. The NPS-WRD summary of water quality for MISS included data 

from 184 stations within park boundaries, 59 of which had exceedances recorded during the 

period of record 1926 - 1994 (National Park Service 1995a). Most of the documented problem 

parameters fall under the categories of dissolved oxygen, metals, or indicator bacteria (Ledder 

2003). Outside of park boundaries, the headwaters of the river are designated as an Outstanding 

Resource Value Water (ORVW) by the state of Minnesota. However, within park boundaries the 

river is on the 2004 Section 303(d) list of impaired waters for aquatic life due to turbidity, 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

4 

Table 1. Water quality monitoring stations with at least five years of data collected by other 

agencies, located within or near MISS park boundaries. USGS = United States Geologic Survey, 

MPCA = Minnesota Pollution Control Agency, WDNR = Wisconsin Department of Natural 

Resources, MCES = Metropolitan Council Environmental Services. 

Agency Station Location (Station ID) Period of 

Record Frequency WQ Parameters 

USGS MissR @ Anoka (05283500) 1973-1982 Monthly Core,nutr,seds 

 MissR nr Anoka (05288500) ¥ 1960-2001 Monthly-to-Qtrly Core,nutr,seds 

 Elm Cr. nr Champlin (05287890) ¥ 1988-present Monthly Core,nutr,seds 

 Shingle Cr. @ Queen Ave. (05288705) ¥ 1996-present Monthly Core,nutr,seds 

MissR @ Robt. Street, UM 839.1 

(05331001) 1938-1972 Monthly Core,nutr,seds 

 MissR @ St. Paul (05331000) ¥ 1967-1981 Monthly Core,nutr,seds 

 MissR @ Hastings (05331580) 1936-present Monthly Core,nutr,seds 

MPCA Crow R. @ Dayton (S-4, CR-0.2) 1953-present 

Quarterly (53-63) 

Monthly (64-79, 90-

04) 

Core,nutr,seds 

 Rum R. @ Anoka (S-16, RUM-0.6) 1953-present Monthly (2 of 5 yrs) Core,nutr,seds 

 MissR @ Anoka (S-25) 1953-2002 Monthly (53-65) 

Biweekly (99-02) Core,nutr,seds 

 Coon Cr. @ 93rd (S-82) 1960-1969 Qtrly-to-Monthly Core,nutr,seds 

 Rice Cr. @ Park (S2-810) 1973-1991 Monthly Core,nutr,seds 

 Rice Cr. @ ERR (S-75) 1960-1965 Quarterly Core,nutr,seds 

 Shingle Cr. @ Lyndale (S-76) 1960-1965 Quarterly Core,nutr,seds 

 MissR @ Mpls Intake (S-24, UM-859) 1953-present Monthly (2 of 5 yrs) Core,nutr,seds 

 MissR @ Coal flats (S1-303) 1998-2004 Weekly Clarity 

 Minnehaha Cr. @ mouth (S-79) 1960-1965 Monthly Core,nutr,seds 

 MnR. @Ft. Snelling Pk. (S-310, MI-3.5) 1974-present Monthly (2 of 5 yrs) Core,nutr,seds 

 MissR @ Wab. Br. (S-266, UM-840) 1973-present Monthly (2 of 5 yrs) Core,nutr,seds 

 MissR @ S. of StP (S-133) 1967-1978 Quarterly Core,nutr,seds 

MissR @ Grey Cloud Is. (S-339, UM826) 1975-present Monthly (2 of 5 yrs) Core,nutr,seds 

 MissR @ Hastings (S-68, UM-815) 1958-present Monthly (2 of 5 yrs) Core,nutr 

WDNR MissR @ Hastings (483026) 1977-1994 Monthly Core,nutr,seds 

MCES Rum R. @ Anoka (RUM-0.6) ?-present Weekly Core 

 MissR @ Anoka (UM-871.6) 1976-present Weekly Core,nutr,seds 

 MissR @ Fridley (UM-862.8) 1978-present Weekly Core 

 Bassett Cr. (BS-1.9) ?-present Monthly Core,nutr,seds 

 Minnehaha Cr. (MH-1.7) ?-present Monthly Core,nutr,seds 

 MissR @ L&D#1 (UM-847.7) 1976-present Weekly Core,nutr,seds 

 Minnesota R. nr mouth (MN-3.5)* ?-present Monthly Core,nutr,seds 

 MissR @ Lamberts Landing (UM-839.1) 1976-present Weekly Core,nutr,seds 

 MissR @ Newport (UM-831.0)* 1980-present Weekly Core,nutr,seds 

 Battle Cr. (BA-0.1) ?-present Monthly Core,nutr,seds 

 MissR @ Grey Cloud (UM-826.7)* 1976-present Weekly Core,nutr,seds 

 MissR @ Spring Lake (UM-821.8) 1982-1991 Weekly (Jun-Sept) Core 

 MissR @ Hastings L&D#2 (UM-815.6)* 1976-present Weekly Core,nutr,seds 

 MissR @ Hastings Hwy (UM-813.9) 1976-2000 Weekly (Jun-Sept) Core 

 MissR @ Hastings RR (UM-812.8) 1977-1991 Weekly (Jun-Sept) Core 

¥ = active USGS streamflow gaging station 

Core = core suite of parameters (dissolved oxygen, specific conductivity, pH, or temperature) 

Nutr = nutrients (total nitrogen, nitrite+nitrate-nitrogen, total kjeldahl nitrogen, or total phosphorus) 

Seds = sediments (suspended sediment, total suspended solids, or turbidity) 

*= core suite monitored on 15-minute intervals 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

5 

aquatic consumption due to mercury and polychlorinated biphenyl (PCB), and aquatic recreation 

due to fecal coliform bacteria (Ledder 2003). Because regional and state regulatory agencies 

monitor regularly (Table 2) for the listed water quality variables, GLKN has chosen to not 

conduct duplicate monitoring for these variables under this protocol. However, the 

bioaccumulative toxics protocols will monitor levels of PCBs, mercury, and other organic 

contaminants in tissues of bald eagles, fish, and potentially other aquatic organisms (Route et al. 

in preparation; Wiener et al. in preparation). 

Figure 1. Map of the Mississippi River within the MISS park unit, 

showing features from the National Hydrography Dataset (NHD). 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

6 

Table 2. Water quality variables and locations of Minnesota 303(d) impaired waters listings 

within MISS, the regulatory agency that monitors that variable, and monitoring frequency. 

Listed Variable Mississippi River Segment (in river miles) Regulatory 

Agency 

Monitoring 

Frequency 

Fecal coliform 

Crow R. to Rum R. (879-871.6) 

Lower St. Anthony Dam to L&D#1 (853-848) 

Minnesota R. to Metro WWTF (844-835) MCES weekly 

PCB FCA 

Crow R. to Lower St. Anthony Dam (879-853) 

L&D#1 to St. Croix R. (848-811) MDNR annually 

Mercury FCA Crow R. to St. Croix R. (879-811) MDNR annually 

Mercury in water Minnesota R. to L&D#2 (844-815) MCES annually 

Turbidity Minnesota R. to St. Croix R. MCES weekly 

PCB = poly-chlorinated biphenyls MCES = Metropolitan Council Environmental Services 

FCA= fish consumption advisory MDNR = Minnesota Department of Natural Resources 

L&D = lock and dam 

Analyses of the data collected by federal, state, and regional agencies and by many independent 

research projects are discussed in a comprehensive review by Lafrancois and Glase (2005). A 

summary of key information relating to MISS follows: 

Ayers et al. (1985) determined that the seasonal rainfall pattern was the most significant 

factor controlling runoff loads in urban, sewered watersheds, while spring snowmelt carried 

the greatest runoff loads in rural watersheds within the larger Twin Cities area. Kroening and 

Andrews (1997) found that nitrogen runoff varied with land use and season: in agricultural 

watersheds runoff peaked in spring and summer, while peak runoff in forested watersheds 

occurred in winter. Kroening (1998) found that nonpoint sources of nutrients dominated all 

sub-basins of the Upper Mississippi River. Highest nutrient and sediment loads were found 

below the confluence of the Minnesota River with the Mississippi River (Kroening et al. 

2002). Kloiber (2004) found that nitrite-nitrate concentrations have increased in the Upper 

Mississippi, according to data collected by the Metropolitan Council Environmental Services 

(MCES) from 1976 to 2002. In contrast, Kloiber (2004) identified declines in biological 

oxygen demand, ammonium, total phosphorus, total suspended solids, and turbidity. 

1.2.2 SACN – St. Croix and Namekagon Rivers 

Stretching from northwest Wisconsin south to the Twin Cities, SACN includes 248 km of the St. 

Croix River and 172 km of the Namekagon River (Figures 2 and 3). The upper reaches of the 

Riverway flow through a largely rural landscape consisting of forests and wetlands. Agricultural 

land use increases as one travels south through the watershed. Urban and suburban development 

also increases southward, until the St. Croix River joins the Mississippi River at Prescott, 

Wisconsin. The lower 41 km of the river, known as Lake St. Croix, function as a lake with a 

retention time of approximately 20 days (Triplett et al. 2003), due to a glacial-age delta at the 

confluence of the two rivers. Lake St. Croix is composed of four distinct pools (Pool 1 is near 

Stillwater, Minnesota and Pool 4 is near Prescott, Wisconsin) caused by narrows or constrictions 

in the river mainstem. Table 3 lists locations that have been monitored by other government 

agencies for at least five years. 
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Figure 2. Map of the St. Croix and Namekagon Rivers within the upper 

portion of SACN. 

Figure 3. Map of the St. Croix River within the lower portion of SACN. 
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Table 3. Historical water quality monitoring stations with at least five years data collected by 

other agencies, located within or near SACN park boundaries. USGS = United States Geologic 

Survey, MPCA = Minnesota Pollution Control Agency, WDNR = Wisconsin Department of 

Natural Resources, MCES = Metropolitan Council Environmental Services. 

Agency Station Location (Station ID) Period of 

Record Frequency WQ Parameters 

USGS Namekagon @ Leonards (05331833) 1995-2002 Monthly (95-98) Core,nutr,seds 

 Namekagon @ Hayward (05331855) 1975-1985 Quarterly Core,nutr,seds 

 Namekagon nr Trego (05332500) ¥ 1966-present Quarterly (76-83) Core,nutr,seds 

 St. Croix R. @ Danbury (05333500) ¥ 1964-present Qtrly (64-67) Mon (76-) Core,nutr,seds 

 Snake R. nr Pine City (05338500) ¥ 1962-1997 Qtrly (76-83, 92-94) Core,nutr,seds 

 St. Croix R. @ SCFalls (05340500) ¥ 1966-present Monthly (74-03) Core,nutr,seds 

 St. Croix R. @ Stillwater (05341550) 1974-1981 Monthly Core 

 Apple R. (05341500) ¥ 1966-1999 Quarterly (76-83) 

Monthly (98-99) Core,nutr,seds 

 Willow R. (05341752) 1998-2002 Monthly (98-99,02) Core,nutr,seds 

Kinnickinnic R. (05342000) ¥ 1968-1999 Monthly (98-99) Core,nutr,seds 

MPCA St. Croix R. nr Danbury (S-56, SC-111) 1957-present Monthly Core,nutr,seds 

 Kettle R. @ mile 11 (S-121, KE-11) 1967-present Monthly Core,nutr,seds 

 Snake R. @ mile 10 (S-198, SN-10) 1971-present Monthly Core,nutr,seds 

 Snake R. @ mouth (S-128) 1967-1971 Monthly Core,nutr,seds 

 Sunrise R. @ MN-95 (S-201, SUN-5) ?-present 

 Sunrise R. @ Sunrise (S-129) 1967-2002 Monthly 

 St. Croix R. @ Osceola (S-57) 1957-1965 Monthly Core, seds 

 St. Croix R. @ Stillwater (S-19, SC-23) 1953-present Quarterly-to-Monthly Core,nutr,seds 

 St. Croix R. @ Hudson (S-126, SC-17) 1967-present Quarterly-to-Monthly Core,nutr,seds 

 St. Croix R. @ Afton (S-918) 1982-1999 Biweekly Core,nutr,seds 

St. Croix R. @ Pt. Douglas (S-18) 1953-1965 Quarterly Core, seds 

WDNR Namekagon R. nr Trego ?-present Monthly, alt. years Core,nutr,seds 

 Totogatic R. nr mouth ?-present Monthly, alt. years Core,nutr,seds 

St. Croix R. @ Pansy Landing (nr 

Danbury) ?-present Monthly Core,nutr,seds 

 U. Tamarack R. ?-present Monthly, alt. years Core,nutr,seds 

 Wood R. nr mouth ?-present Monthly, alt. years Core,nutr,seds 

 St. Croix R. @ Interstate (nr SCFalls) ?-present Monthly Core,nutr,seds 

Lower Willow R. nr mouth ?-present Monthly, alt. years Core,nutr,seds 

MCES St. Croix R. @ Stillwater (SC 23.3) 1976-present Weekly Core,nutr,seds 

 St. Croix R. @ Prescott (SC 0.3) 1976-present Weekly Core,nutr,seds 

 Browns Cr. (BR 0.3) 1998-present Monthly, storms Nutr,seds 

 Little Carnelian L. outlet (CM 3.0) 1995-present Monthly, storms Nutr,seds 

 Silver Cr. (SI 0.1) 1998-present Monthly, storms Nutr,seds 

 Valley Cr. (VA 1.0) 1999-present Monthly, storms Nutr,seds 

¥ = active USGS streamflow gaging station 

Core = core suite of parameters (dissolved oxygen, specific conductivity, pH, or temperature) 

Nutr = nutrients (total nitrogen, nitrite+nitrate-nitrogen, total kjeldahl nitrogen, or total phosphorus) 

Seds = sediments (suspended sediments, total suspended solids, or turbidity) 
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Six USGS streamflow gages currently operate within or near SACN park boundaries: on the 

Namekagon River near Trego, Wisconsin (site #05332500, 1927-present); on the St. Croix River 

at Danbury, Wisconsin (site #05333500, 1914-present), near Grantsburg, Wisconsin (site 

#05336000, 1923-present), and St. Croix Falls, Wisconsin (site #05340500, 1902-present); on 

the Apple River near Somerset, Wisconsin (site #05341500, 1914-1970 and 1986-present); on 

the Kinnickinnic River (site #05342000, 1916-present); and on the Mississippi River at Prescott, 

Wisconsin (site #05344500, 1928-present). 

Pressures potentially affecting water quality of the Namekagon and St. Croix Rivers include 

industrial and wastewater discharge; stormwater and agricultural runoff; nutrient loading from 

tributaries, agriculture, forestry; and recreational use (Ledder 2003; Lafrancois and Glase 2005). 

The NPS-WRD summary of water quality for SACN covered the period of record from 1926 to 

1995 (National Park Service 1995b). The summary includes data from 469 monitoring stations in 

the study area, of which 107 are within park boundaries. Several (14) parameters were recorded 

to have exceeded EPA criteria at least once for freshwater aquatic life or drinking water at 22 

stations within park boundaries. 

Lafrancois et al. (in press) have analyzed the trends in concentrations and loadings from 29 years 

of monitoring data for Lake St. Croix (St. Croix River between Stillwater, Minnesota and 

Prescott, Wisconsin), within SACN, and for Lake Pepin, which is immediately downstream of 

both MISS and SACN. Total phosphorus (TP), orthophosphate, ammonia-N, and sediment 

concentrations and loads have decreased since the 1970s, but nitrate+nitrite-nitrogen and total 

nitrogen have increased over the same period. Although TP concentrations in Lake St. Croix 

have decreased slightly over the last few decades, monitoring in the last decade (1998-2006) 

indicated that TP exceeds EPA guidelines for determination of use support for lakes. As a result, 

both Minnesota and Wisconsin added Lake St. Croix to their 2008 303(d) lists for excessive 

nutrients. 

Although most of the exceedances occurred prior to the 1990s (National Park Service 1995b), 

the St. Croix River below St. Croix Falls is on Wisconsin’s Section 303(d) for aquatic 

consumption due to PCBs (Ledder 2003). The entire section of the St. Croix River within 

Minnesota is on the state’s 303(d) list for aquatic consumption due to mercury. Because regional 

and state regulatory agencies monitor regularly (Table 4) for the listed water quality variables, 

GLKN has chosen to not conduct duplicate monitoring for these variables. As mentioned above, 

the bioaccumulative protocols will monitor several contaminants in animals that are high in the 

food chain (Route et al., in preparation; Wiener et al., in preparation). Despite the 303(d) listings, 

the state of Wisconsin has designated the Namekagon River and the majority of the St. Croix 

River as outstanding resource waters (ORW). Further, the St. Croix River at St. Croix Falls and 

from Hudson, to Prescott, is designated as exceptional resource waters (ERW; high quality 

resource subject to point source pollution) by the state of Wisconsin. The state of Minnesota has 

designated the entire section of the St. Croix River within state boundaries as outstanding 

resource value waters (ORVW). 
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Table 4. Water quality variables and locations of Minnesota (MN) and Wisconsin (WI) 303(d) 

impaired waters listings within SACN, the regulatory agency that monitors the variable, and 

monitoring frequency. 

State Listed Variable St. Croix River Segment (in river miles) Regulatory 

Agency 

Monitoring 

Frequency 

MN Mercury FCA MN/WI border to Prescott (127-0) MDNR annually 

WI PCB FCA St. Croix Falls to Prescott (52-0) WDNR/MDNR annually 

MN/WI Total Phosphorus Stillwater, MN to Prescott (25 – 0) WDNR/MDNR annually 

FCA= fish consumption advisory WDNR = Wisconsin Department of Natural Resources 

PCB = poly-chlorinated biphenyls MDNR = Minnesota Department of Natural Resources 

Analyses of the data collected by federal, state, and regional agencies, and by many independent 

research projects, are discussed in a comprehensive review by Lafrancois and Glase (2005). A 

summary of key information relating to SACN follows: 

Lenz (2004) analyzed St. Croix River flow data from USGS gages at Danbury (1914-2003) 

and St. Croix Falls (1902-2003), noting increasing stream flows at both sites over the past 

century. Agricultural streams carried much more nitrogen and phosphorus than did forested 

or urban streams in the St. Croix basin (Fallon and McNellis 2000). Phosphorus loading in 

the St. Croix River has decreased slightly over the last 30 years, but current conditions far 

exceed EPA Ecoregion VII reference conditions (Lafrancois et al. 2004). About 90% of the 

phosphorus loading appears to derive from nonpoint sources, while nitrate levels have 

increased over the last 30 years (Lenz et al. 2003). Kloiber (2004) found that dissolved 

oxygen and nitrite-nitrate concentrations have increased in the Lower St. Croix, according to 

data collected by the Metropolitan Council Environmental Services (MCES) from 1976 to 

2002. In contrast, Kloiber (2004) identified declines in biological oxygen demand, 

ammonium, total Kjeldahl nitrogen, fecal coliform bacteria, total suspended solids, and 

turbidity. 

1.3 Measurable Objectives 

Our overall goal is to develop a protocol for monitoring water quality in large rivers that will 

contribute to an understanding of the ecological integrity of park units of the Great Lakes 

Network. Specifically, this protocol is designed to document river water quality status and trends 

for individual stations, on a longitudinal (downstream) basis, and a park-wide basis. The protocol 

includes historical analysis, sample design, field and laboratory methods, data analysis and 

reporting, and training and operational requirements. The protocol objectives and specific 

monitoring questions are outlined below. 

1.3.1 Protocol Objectives 

1) Gather flow data for the St. Croix, Namekagon, and Mississippi Rivers to determine 

changes in mean monthly and mean annual flows. 

2) Monitor mean annual concentrations of core and advanced suite parameters in MISS and 

SACN and from the mouths of selected tributaries, accounting for seasonality in water 

quality conditions. 
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3) Relate current water quality conditions to known historical conditions. 

4) Analyze water quality parameters for trends, and correlate any observed trends with 

potential causes (such as weather, climate, land use, point sources, exotic species, and 

atmospheric deposition). 

1.3.2 Monitoring Questions for the Main Stems of the Mississippi, St. Croix, and 

Namekagon Rivers Within MISS and SACN 

1) What are the current status and long-term trends in systematic flow regime? 

2) What are the current status and long-term spatial and temporal trends in select water 

quality variables, including temperature, pH, specific conductance, dissolved oxygen, 

water clarity, sediment, alkalinity, major ions, and nutrients? 

3) Are changes in water quality parameters correlated with tributary influences or changes 

in other aspects of the ecosystem, such as measures of biotic communities, exotic species, 

land use or land cover, weather and climate, or atmospheric deposition? 

1.4 Quality Assurance and Quality Control 

Quality assurance is the planned and systematic pattern of all actions necessary to provide 

adequate confidence, or assurance, that a project outcome optimally fulfills expectations. Quality 

control is the systematic evaluation of the various aspects of a project to ensure, or control, that 

the standards of quality are being met. Quality control involves specific tasks undertaken to 

determine the reliability of field and laboratory data. Together, quality assurance/quality control 

(QA/QC) is a significant part of any monitoring program. The objective of QA/QC is to ensure 

that the data generated by a project are meaningful, representative, complete, precise, accurate, 

comparable, and scientifically defensible (O’Ney 2005). It is a broad management concept for 

maintaining the ability to provide reliable information, requiring the complete integration of field 

and laboratory systems of sample collection and analysis. Therefore, QA/QC incorporates 

peripheral but essential operations such as survey design, equipment preparation, maintenance 

tasks, data handling, and personnel training; it is summarized throughout every aspect of this 

monitoring protocol. 

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2.0 Sampling Design 

2.1 Rationale for Selecting this Sampling Design Over Others 

Two major ecological monitoring programs (the USGS National Water-Quality Assessment 

[NAWQA] program and the EPA Environmental Monitoring and Assessment Program-Aquatic 

Resource Monitoring [EMAP-ARM]) use different site-selection methods (summarized below). 

Our goal is to combine the strengths of both programs for monitoring water quality of lotic 

systems in the NPS Great Lakes Network. 

2.1.1 USGS NAWQA Program Site-Selection Method 

The USGS National Water-Quality Assessment (NAWQA) program is designed to assess the 

current status and long-term trends of the water quality of the nation’s water resources. The study 

units (each about 10,000 km2

) cover a major portion of the nation, and research focuses on 

hydrologic and ecologic resources that are under agricultural and urban influences. The status of 

water quality conditions is assessed in two- to three-year intensive studies, while long-term 

trends in water quality are assessed by repeated intensive studies every 10 years. 

Gilliom et al. (1995) summarize the NAWQA design and site-selection method as follows. 

Water-quality sampling is conducted at two types of fixed sites: integrator and indicator. 

Integrator sites, located at major intersections in the drainage network, are chosen to represent 

water-quality conditions in heterogeneous, large basins that are often affected by complex 

combinations of land-use settings, point sources, and natural influences. Indicator sites, in 

contrast, are chosen to represent water-quality conditions in relatively homogeneous smaller 

basins (50-500 km2) associated with specific individual environmental settings. Each study unit 

typically contains 3-5 integrator sites and 4-8 indicator sites (Figure 4). Depending on the water 

quality variable, sampling occurs on a continuous, fixed-interval (usually monthly), or extremeflow basis. 

In addition to the fixed-site locations, NAWQA study units may contain synoptic sites designed 

to increase the spatial resolution of data for the highest-priority water-quality issues. Sites are 

located to provide balanced spatial coverage at the desired resolution in the target geographic 

area and near stream junctions to facilitate mass-balance analysis for the sampling period. 

2.1.2 EPA EMAP-ARM Program Site-Selection Method 

In theory one could design a comprehensive monitoring program that directly measured the 

current and changing conditions of river water quality. However, such a census of the entire 

‘population’ of water quality samples would be cost-prohibitive. McDonald and Geissler (2004) 

posit that judgment sampling, or using ‘representative’ sites selected by experts, is inappropriate 

for long-term monitoring projects because this method of sample design can produce biased, 

unreliable information. Statistical sampling methods are efficient for broad spatial domains 

because they require sampling fewer locations to make valid scientific statements about 

conditions across large areas. In addition, the statistical design of a project should precede data 

collection to maximize budget and minimize bias (Ward et al. 1990). 
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Figure 4. Geographic distribution of environmental settings and sampling sites 

within a NAWQA study unit (White River Basin, Indiana; from Fenelon 1998). 

All streamwater within a watershed at a given moment in time represents a statistical population. 

Random sampling from the population allows for scientifically valid inferences to be made about 

the current and changing conditions of the watershed. Through stratification, the entire 

population is divided into any number of sub-populations (strata). Random sampling within each 

stratum allows statistical inferences to be made about each stratum. For example, sampling from 

particular tributaries could make it possible to monitor the effect of distinct land uses within 

those subwatershed areas. Generally, stratification seeks to minimize within-stratum variability 

by maximizing variability among pre-defined groups. 

McDonald et al. (2002) summarize the site-selection method of EMAP as follows. The method 

proceeds from a generalized random tessellation stratified (GRTS) design (Stevens and Olsen 

2004). Stream networks are identified on 1:100,000 scale maps, including the length and stream 

order of each stream segment. If equal numbers of samples from each stream order are desired, 

then differential weighting by size may be necessary, due to the predominance of lower-order 

streams. For example, weighting factors of 1, 2, and 4 could be used to produce similar-sized 

statistical samples for first-, second-, and third-order streams, respectively. 

Using this weighting scheme, the inclusion probability for a stream segment is proportional to its 

segment length times the weight of its stream order. Segment lengths are multiplied by their 

weight, sorted randomly, then organized in a single continuous line (Figure 5). The minimum 

number of water samples that need to be collected from a population or stratum are determined 

by the analytical precision required to identify changes in water quality (see section 2.4). The 

selection length is determined by dividing the length of the randomly-sorted line by the number 
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of samples needed. The selection of sites begins with a random point on the first segment, and 

proceeds by measuring off the selection length along the randomly-sorted line. In this way, the 

site-selection method not only identifies which stream segments are to be sampled, but at what 

point on the segment the sample is to be located. 

Figure 5. Example of a random statistical sample selection process for 

stream networks (from Olsen 2002). 

2.1.3 GLKN Program Site-Selection Method 

This program is designed to monitor the water quality of the Mississippi, St. Croix, and 

Namekagon Rivers within the boundaries of MISS and SACN. Unlike the USGS and EPA study 

units, these NPS parks do not include the entire watershed but rather are linear features 

containing sections of the mainstem river, riparian lands, and the mouths of tributaries (Figure 

6). Geographic stratification of the population by subwatersheds and stream-order weighting do 

not apply in this case. 

Random Versus Nonrandom Site-Selection: The monitoring objectives drive the site-selection 

process. The objective to determine population statistics, such as mean annual concentrations, 

requires randomly-selected sites. The objective to track the influence of individual tributaries 

(and land uses) requires nonrandomly-selected sites. As discussed earlier, we aim to incorporate 

the practical strengths of the USGS and EPA designs into the monitoring design of the Great 

Lakes Network’s river water quality program. Specifically, we plan to employ a random siteselection similar to the EPA method, and make use of nonrandom site-selection similar to the 

USGS method. 
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Figure 6. Schematic diagram of National Park Service park unit centered on a major river and 

covering a small portion of the watershed. The park unit (shaded green) contains a section of the 

mainstem river and riparian lands. Random EMAP-type stations (solid circles) and nonrandom 

NAWQA-type stations (open circles) are depicted. 

Random site-selection along the mainstem using statistical methods can ensure scientificallyvalid assessments of mainstem river water quality. Therefore, a set of randomly-selected 

monitoring sites is needed to define the population characteristics, in spite of existing efforts of 

other agencies to monitor long-term mainstem water quality at particular locations (see Section 

1.2). Installation of a new set of random sites, independent of another agency’s monitoring 

budget, will help to ensure GLKN collects a consistent dataset with which to assess long-term 

water quality trends. 

Nonrandom site-selection can help to identify water quality trends at locations of high interest. 

Tributaries often influence water quality within the mainstem (e.g., the influence of the 

Minnesota River on the upper Mississippi), and it will be important to monitor the contributions 

of tributaries. In addition, particular mainstem locations may be deemed important monitoring 

sites. For example, no monitoring program has ever monitored the downstream end of the MISS 

park unit, where mixing of the St. Croix and Mississippi Rivers occurs. 

This program will include both randomly-selected and nonrandomly-selected sites. All sites will 

be analyzed on an individual basis, to determine water quality trends at each location. Only the 

randomly-selected sites will be grouped for analysis of population statistics and trends. 

Stratification to Reduce Population Variability: Stratification is employed to reduce the 

variability in a selected population. Although this water quality monitoring program will not 

cover entire subwatersheds, the method of stratification described previously is still desirable for 

the two large river parks in the Network, as they have distinctive geographic features within the 

parks that serve to increase the variability of water quality data. 

SACN: The St. Croix River is known to have a gradient of decreasing water quality as one 

travels downstream, due in part to distinctly different land uses and land covers in the upper and 

lower portions of the watershed. Forests and wetlands cover the upper portion of the St. Croix 

watershed, and streams are rocky and dynamic, whereas agricultural and urban lands dominate 

the lower portion, and the river widens to form a riverine lake (Figure 7). However, the 
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geographic distribution of these land uses has and will continue to change with time. Consistent 

characterization of an ecological resource requires that it be stratified based on a feature that will 

not change with time (Stevens and Olsen 1991). Therefore, we stratified the river based on 

hydrological processes rather than land use. Our stratification was between the mainstem of the 

St. Croix River above Stillwater, Minnesota, and the riverine lake (St. Croix River below 

Stillwater, known as Lake St. Croix). Fundamental differences exist in the hydrological 

processes of these two portions of the river; the slower residence time of Lake St. Croix makes it 

behave more like a lake, very differently than classic mainstem river flow. This difference in 

flow behavior leads to different outcomes in water quality, detailed below, in the discussion on 

power analysis. 

Figure 7. Land cover of the St. Croix River basin. 

MISS: We stratified the Mississippi River within park boundaries into four segments (listed by 

river mile): UM-878 to UM-845, UM-845 to UM-836, UM-836 to UM-813, and UM-813 to 

UM-807. These segments are delineated by three major features within the river corridor that are 

known to have strong influence on the water quality of the Mississippi River: 1) the confluence 

of the Minnesota River (at river mile UM-845), which is the single largest point source of 

sediments and nutrients to the Upper Mississippi River; 2) the Twin Cities metropolitan 
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wastewater treatment facility, which discharges phosphorus and nitrogen to the Mississippi River 

below St. Paul, Minnesota (at river mile UM-836); and 3) the confluence of the St. Croix River 

(at river mile UM-813), which exerts dilution on Mississippi River water quality. Each of these 

long-term features fundamentally changes the hydrology of the Mississippi River. 

 

2.2 Site-Selection 

2.2.1 Procedures for Random Site-Selection 

(modified from: www.epa.gov/nheerl/arm/designpages/design_tech_info.htm#DesignTech) 

1) Determine the minimum number of random sites required to achieve the desired level of 

precision (see section 2.4, below). Double the size of the selection pool to accommodate 

oversampling (enabling the ability to eliminate inaccessible sites, or adding future sites, 

etc.). 

2) Measure the length of mainstem river within the park unit to be sampled. 

3) Calculate selection length by dividing river length by the number of sites in the selection 

pool. 

4) Identify the individual reaches of the river and re-order the reaches into a randomlysorted line. 

5) Randomly select a site within the first reach in the line. 

6) Proceed along the randomly-sorted line, selecting sites spaced one selection length from 

each other. 

7) From the resulting selection pool, randomly select half of the stations; these are the 

randomly-selected monitoring sites. 

8) If one of the randomly-selected locations is physically inaccessible, choose the next 

location from the selection pool. 

9) Additional considerations (Stednick and Gilbert 1998): sampling locations on the 

mainstem should be located a distance of five stream widths below the influence of a 

tributary to ensure adequate mixing; stations with continuous flow monitoring are 

preferred; if this is not possible, stations should be located along a straight and narrow 

reach with minimal channel complexity. 

2.2.2 Criteria for Nonrandom Site-Selection 

In general, the goal of nonrandom site-selection for MISS and SACN is to fill gaps in the 

existing monitoring networks of other agencies, especially at locations that have historical 

monitoring data, in order to improve the datasets for all agencies. The St. Croix Basin Water 

Resources Planning Team (hereafter called the Basin Team), composed of federal, state 

(Minnesota and Wisconsin), and regional water resources professionals who are actively 

involved in management of the St. Croix River basin, is developing a comprehensive monitoring 

plan for the St. Croix River that incorporates the existing monitoring efforts of various agencies. 

The monitoring plan will identify the gaps in existing efforts and the needs for additional 

monitoring, with a focus on a goal of a 20% reduction in phosphorus loading. The Basin Team 

Nutrient Subcommittee identified gaps in the current monitoring programs and recommends the 

following criteria, in order of priority, for selecting nonrandom sites in the St. Croix basin: 

1) Add monitoring stations along the mainstem of the St. Croix River, particularly in the 

lower portion that includes Lake St. Croix. 
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2) Some existing monitoring stations (e.g., USGS gaging stations) are monitored for water 

quality on a quarterly basis or not at all; supplement monitoring at these locations with a 

higher frequency of sampling. 

3) Resume monitoring at the mouth of tributaries that have a history of previous monitoring, 

particularly if the tributary has a nearby upstream gaging station. 

4) Target tributaries without a monitoring history if significant water quality changes are 

occurring or are expected to occur in the future. 

2.3 Historical Variability and Statistical Power Analysis 

Large rivers often exhibit variations in flow and subsequent variations in water quality due to 

climate seasonality, geology, geography, dominant vegetation, and land use. All of these factors 

contribute to the storm water runoff and baseflow characteristics of subwatersheds. As a rule, 

river systems respond more dynamically to fluctuating runoff than do lake systems. By virtue of 

their longer residence times, lakes tend to modulate the effects of water quality variability in 

runoff; collecting relatively few samples during a year can be sufficient to define the average 

water quality conditions for that year. In contrast, a river drainage network is a flow-through 

system, efficiently delivering dynamic pulses of runoff from the land surface to waterways. In 

addition, river water quality will reflect the seasonal fluctuations in runoff water quality. As a 

result, large rivers require a much higher sampling frequency than lakes in order to define the 

average water quality conditions. 

The variations in historical sampling frequencies make it challenging to determine if water 

quality changes have occurred with time. Statistical power analysis assesses the ability of a 

hypothesis test to detect a change, given that change actually exists. We conducted statistical 

power analysis on St. Croix River historical data to test the power of the historical monitoring 

efforts to detect a 20% change, using an on-line calculator (http:// calculators.stat.ucla.edu 

/powercalc /normal /n-1/) shown in Figure 8. This calculator has been found to match the results 

of the Zar (1999) equations. However, these types of calculators assume a normal distribution to 

the data and tend to overestimate the power and underestimate the sample size of skewed data. 

Statistical power (1-β) increases as sample size (n), minimum detectable change or effect size 

(d), or specified significance-level (α) increases, and declines as the population variance (σ) 

increases. Effect size (e.g., 20% change), often called minimum detectable difference (MDD) is 

the difference between the null and alternative hypotheses (μo and μa), and can be measured 

either using raw or standardized values. Raw measures, such as the difference between means 

(μa-μo) or slope in a regression analysis, are closer to the measurements that researchers take and 

hence are easier to visualize and interpret (Thomas and Krebs 1997). Thus, statistical calculators 

of this type require the input of five parameters (n, α, 1-β, μo, σ, or μa) in order to solve the sixth. 

We evaluated the possibility of reducing variability by limiting sampling to narrow index times 

of the year. Using the historical data, we conducted power analysis on monthly and quarterly 

means of selected water quality variables. Across sites and parameters, there were no 

consistently ‘better’ periods of the year for reducing variability in the sampled data. In addition, 

this large rivers protocol is designed for analysis of long-term trends in annual means, rather than 

the trend in a small portion of the year (for example, only sampling in August). As a natural 

resource, large rivers are highly variable, and it is important to observe their behavior throughout 

the entire year. 
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Normal Power Calculations

Normal Distribution 1-Sample 

Enter a "?" for the item to be calculated. 

μ 0 

 The Mean of the Distribution under the Null Hypothesis 0.057 

μ a 

 The Mean of the Distribution under the Alternative Hypothesis 0.068 

Sigma

 The Standard Deviation of the Population 0.0137 

N

 The Sample Size 3 

Significance Level

 The Significance Level of the test or Prob (reject null hypothesis 

(H 0 : μ=μ 0 ) given it is true) 

0.05 

Power

 The Power desired for the test or Prob (reject H 0 given that H a is 

true) 

? 

Number of Sides

 Specifies Alternative Hypothesis. 

 One sided and μ a > μ 0 => H a : μ > μ 0 

 One sided and μ a < μ 0 => H a : μ < μ 0 

 Two sided => H a : μ not equal μ 0 

1 Side 

2 Sides 

Calculate

The Power is calculated to be 0.134 

Figure 8. Screen snap-shot of on-line statistical power calculator 

(http://calculators.stat. ucla.edu/ powercalc/ normal/ n-1/). Alternative 

hypothesis was defined as 20% change from population mean. 

2.3.1 SACN 

The historical data were stratified between three stations in the upper St. Croix basin (Trego, 

Danbury, and St. Croix Falls) and three stations in the lower St. Croix basin (Stillwater, Hudson, 

and Prescott). Three water quality variables (pH, dissolved oxygen, and total phosphorus) were 

chosen to represent low, moderate, and high variability data, respectively. Based on the 30-year 
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mean values, DO concentration was greater and pH and TP levels were lower in the Upper St. 

Croix than in the Lower St. Croix. 

Annual means were calculated from all available data for each parameter for each of 30 years 

(1974-2003) for each station. The individual annual means for each group of three stations were 

used to calculate 30 annual means and coefficients of variation (CVs) for the upper and lower 

portions of the basin. Because each of the annual statistics was derived from one value per 

station, the result is a measure of the range of variability among stations, providing the valid 

basis from which to calculate sample size. To gage the range of variability, the 30-year 

minimum, mean, and maximum values of the annual statistics were evaluated in the power 

analysis. Table 5 lists the minimum, mean, and maximum of the annual mean and CVs in the 

upper and lower portions of the basin, and the power of previous monitoring efforts to detect 

change. Over the range of variation observed in pH and dissolved oxygen, the sampling 

frequency of historical monitoring was sufficient to achieve the goal of 70-80% power of 

detecting 20% change. In contrast, the historical monitoring efforts had very low power to detect 

change in total phosphorus, due to the higher observed variation for this water quality variable. 

Table 5. Within the upper and lower portions of the SACN park unit, the 30-year minimum, 

mean, and maximum values of the annual mean and coefficient of variation (CV, %), and the 

statistical power (%) of historical monitoring efforts to detect a 20% change (n = 3), based on the 

annual means (1974-2003) of three water quality variables: pH (standard units), dissolved 

oxygen (DO, mg/L), and total phosphorus (TP, mg/L). Two-tailed significance level α2 = 5%. 

 Upper St. Croix Lower St. Croix 

 Statistic pH DO TP pH DO TP 

Min Value Annual Mean 6.85 8.32 0.018 7.42 8.45 0.036 

 CV (%) 0.2 1 3 0.04 2 1 

 Power (%) 100 100 91 100 100 100 

Mean Value Annual Mean 7.55 9.55 0.041 7.70 9.48 0.057 

 CV (%) 2 5 34 0.6 7 24 

 Power (%) 100 90 9 100 75 13 

Max Value Annual Mean 8.20 11.33 0.071 8.14 11.77 0.094 

 CV (%) 9 12 95 3 21 98 

 Power (%) 53 35 4 100 16 4 

2.3.2 MISS 

Six historical water quality monitoring stations administered by other agencies are located within 

the first three of the four Mississippi River segments. These six stations have 26-year historical 

records of pH, dissolved oxygen, total phosphorus, and nitrate-nitrogen data since 1980 (Table 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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6). Unfortunately, no agency has ever monitored along the fourth segment, so the historic mean 

and variability of water quality at the downstream end of the park unit are unknown. Based on 

the 26-year mean values for the first three segments, the downstream spatial trend of water 

quality through the MISS corridor is one of decreasing pH and DO, and increasing TP and 

nitrogen-oxides (NOx-N). 

Annual means and standard deviations of the four variables were used to derive 26-year means 

and standard deviations. Care was taken to ensure that the calculated standard deviations were a 

measure of the variability among stations. Power analysis was conducted 1) on the entire dataset 

(n = 6) representing historical water quality in the entire park unit corridor, and 2) on two subsets 

(n = 2 and n = 3) representing the water quality in two segments of the park unit corridor (Table 

7). Power analysis, which requires a measure of population variability, was not conducted on one 

of the segments because it contained only one historical monitoring station. 

Table 6. The 26-year mean values of annual mean and coefficient of variation (CV, %) for 

monitored portions of the MISS park unit, and the statistical power (%) of historical monitoring 

efforts to detect a 20% change, based on the annual means (1980-2005) of four water quality 

variables: pH (standard units), dissolved oxygen (DO, mg/L), total phosphorus (TP, mg/L), and 

nitrogen oxides (NOx-N, mg/L). 

(-- = data not available.)

River Segment Statistic pH DO TP NOx-N 

MISS 878-845 Mean 8.06 10.50 0.103 0.73 

(n=2) CV (%) 0.7 7 13 25 

 Power (%) 99.7 25 12 7 

MISS 845-836 Mean 8.03 10.08 0.157 1.98 

(n=1) -- -- -- -- -- 

MISS 836-813 Mean 7.97 9.78 0.228 2.28 

(n=3) CV (%) 0.5 3 8 4 

 Power (%) 100 100 56 98 

MISS 813-807 -- -- -- -- -- 

(n=0) -- -- -- -- -- 

MISS 878-807 Mean 8.01 10.07 0.175 1.71 

(n=6) CV (%) 0.9 6 38 47 

 Power (%) 100 100 20 14 

Three pieces of evidence point to the existence of separate populations of water quality along the 

MISS corridor. First, two-sample comparisons (http:// calculators.stat.ucla.edu/ twosamp/) of the 

first three segments revealed three distinct populations of water quality; p-values were generally 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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small (Table 7). Second, for each segment, the variability among stations is less than the 

variability among years. Third, stratification into separate subpopulations (n = 2 and n = 3) 

appears to decrease the variability observed in the entire (n = 6) set of monitoring data (Table 6). 

In summary, the information goals and statistical requirements determine the sampling 

frequency. To identify the long-term trends in a stream or river, the sampling frequency should 

be sufficient to identify a statistical trend beyond the background variability of a dynamic flow 

system. Therefore, it is essential to evaluate existing data prior to establishing 1) the number of 

sites and 2) the frequency of sampling. Statistical power analysis based on the power to detect 

change will guide the selection of these two parameters, using calculations of statistical sample 

size and analysis of sensitivity to sampling frequency, respectively. 

Table 7. Two-sample comparisons based on 26 annual means for pH (standard units), dissolved 

oxygen (DO, mg/L), total phosphorus (TP, mg/L), and nitrogen oxides (NOx-N, mg/L). 

Statistic pH DO TP NOx-N 

Comparison: Segment 1(879-845) vs. Segment 2 (845-836) 

T-stat 0.68 2.68 -6.43 -6.48 

P-value 0.499 0.011 <1E-6 1E-6 

Comparison: Segment 2(845-836) vs. Segment 3 (836-813) 

T-stat 1.98 1.82 -6.37 -1.28 

P-value 0.053 0.076 <1E-6 0.207 

Comparison: Segment 1(879-845) vs. Segment 3 (836-813) 

T-stat 2.50 6.43 -13.2 -9.47 

P-value 0.016 <1E-6 <1E-6 <1E-6 

2.4 Number and Location of Monitoring Stations 

The National Park Service-Water Resources Division (NPS-WRD) has recommended that 

roughly two-thirds of selected sites should be located within either Section 303(d)-impaired 

waters or pristine waters that the park seeks to preserve (Irwin 2004). All of the St. Croix and 

Namekagon Rivers within SACN have been designated as outstanding or exceptional waters by 

Minnesota and Wisconsin (see Section 1.2.2). A portion of the St. Croix River, from where it 

enters Minnesota down to Prescott, is on the 303(d) list. In addition, a majority of the tributary 

mouths that might potentially be monitored as part of the nonrandomly-selected sites are either 

pristine or impaired. All of the Mississippi River within MISS is on the 303(d) list, and none of it 

is designated as outstanding waters by Minnesota (see Section 1.2.1). Therefore, we expect that 

1) all of the randomly-selected sites for SACN, 2) the majority of the nonrandomly-selected sites 

for SACN (see Table 10), and 3) all of the sites selected for MISS, will be located within pristine 

or impaired waters. 

2.4.1 Randomly-Selected Stations Within SACN 

When planning a study, statistical power analysis is most useful to: 1) explore the relationships 

between the range of statistical sample sizes that are deemed feasible, 2) determine the effect 

size, or minimum detectable change thought to be biologically important, 3) calculate levels of 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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variance that could exist in the population, and 4) establish desired levels of error risks (α and β) 

(Thomas and Krebs 1997). The outcome of such analysis is a decision about statistical sample 

size and target effect size, or conversely, whether a study is worth pursuing based on an expected 

sample size limit. NPS-WRD recommends conducting sample size analysis using a multi-step 

approach, and to “consider throwing out variables where the variability in pristine sites is so high 

that one would never find a trend or effect size of biological concern given funding limitations” 

(Irwin 2004). 

Estimation of the number of sites needed, or statistical sample size analysis, was conducted using 

the observed variation in the historical monitoring data for the St. Croix River. The on-line 

statistical sample size calculator (http://calculators.stat.ucla.edu/ powercalc/normal/n-1/) was 

used to determine the number of sites needed to detect 20% change at 80% power and 5% 

significance, summarized in Table 6, above. For pH and dissolved oxygen, the range of observed 

variation is small enough to require relatively few monitoring sites. In contrast, the mean CV of 

total phosphorus requires 40 monitoring sites in the St. Croix basin — far more than the GLKN 

monitoring budget allows. 

Based on the historical data, it is not possible to monitor total phosphorus to detect 20% change. 

Therefore, we have made the decision that the GLKN large rivers monitoring program will seek 

to detect 20% change in low to moderate variability parameters of the St. Croix River. 

Accordingly, the sample size analysis (Table 8) indicates that three stations in each of the upper 

and lower portions of the St. Croix basin should be sufficient to monitor the long-term average 

water quality conditions. Thus, there will be six randomly-selected monitoring sites within 

SACN. 

The random site-selection process resulted in three upper SACN stations (Namekagon River near 

Earl, Wisconsin, St. Croix River near Norway Point, and St. Croix River near the confluence 

with the Trade River) and three lower SACN stations on the St. Croix River (Pool 1 near 

Bayport, Minnesota, Pool 2 near Lake St. Croix Beach, Minnesota, and Pool 4 near Prescott, 

Wisconsin). The random site-selection process included oversampling (see Section 2.2.1), so that 

if any of the stations are deemed as inappropriate monitoring sites, there are more locations from 

which to choose. The oversampled sites are in the upper SACN (Namekagon River at Squaw 

Bend Bridge, Namekagon River at Groat Landing, and St. Croix River at Stillwater, Minnesota) 

and the lower SACN on the St. Croix River (Pool 1 near Stillwater, Minnesota, Pool 3 near 

Afton, Minnesota, and Pool 4 below the confluence with the Kinnickinnic River). 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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Table 8. Within the upper and lower portions of the SACN park unit, the 30-year minimum, 

mean, and maximum values of the annual mean and coefficient of variation (CV, %), and the 

predicted sample size (number of sites) required to detect a 20% change at 80% power, based on 

the annual means (1974-2003) of three water quality variables: pH (standard units), dissolved 

oxygen (DO, mg/L), and total phosphorus (TP, mg/L). Two-tailed significance level α2 = 5%. 

 Upper St. Croix Lower St. Croix 

 Statistic pH DO TP pH DO TP 

Min Value Mean 6.85 8.32 0.018 7.42 8.45 0.036 

 CV (%) 0.2 1 3 0.04 2 1 

 Sample size 1 1 1 1 2 4 

Mean Value Mean 7.55 9.55 0.041 7.7 9.48 0.057 

 CV (%) 2 5 34 0.6 7 24 

 Sample size 2 3 26 1 3 14 

Max Value Mean 8.20 11.33 0.071 8.14 11.77 0.094 

 CV (%) 9 12 95 3 21 98 

 Sample size 4 5 187 2 11 190 

2.4.2 Nonrandomly-Selected Stations Within SACN 

The Network will include as many as five nonrandomly-selected sites within SACN, depending 

on the annual budget. Potential locations, given as river miles on the Namekagon (NAM) or St. 

Croix (SC) Rivers, of nonrandomly-selected monitoring stations are listed below, including the 

reason for possible inclusion: 

1) NAM 98 – Nearest of headwaters of SACN, at Namekagon Dam 

2) NAM 35 – USGS gaging station at Trego (*) 

3) SC 96 – Mouth of Kettle R., downstream from active USGS gage 

4) SC 92 – Mouth of Snake R., downstream from active USGS gage 

5) SC 70.5 – Mouth of Sunrise R., MPCA samples only 2 of 5 yrs (*) 

6) SC52 – St. Croix Falls, active USGS gaging station not monitored (*) 

7) SC 30 – Mouth of Apple R., downstream from active USGS gage (*) 

8) SC 17 – Mouth of Willow R., downstream from active USGS gage (*) 

9) SC 13 – Pool 2 of Lake St. Croix – supports modeling efforts 

10) SC 8 – Pool 3 of Lake St. Croix - supports modeling efforts 

11) SC 6 – Mouth of Kinnickinnic R., downstream from active USGS gage (*) 

(*) = highly recommended by St. Croix Basin Team, in order to fill gaps in current 

monitoring by other agencies. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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An additional two sites are of particular interest to SACN staff: one on the Namekagon River and 

the other on the upper St. Croix River downstream from a cranberry farm. These two sites will 

be included in the monitoring design as funding permits. Figure 9 shows the selected GLKN 

monitoring sites for SACN, including the six randomly-selected sites, the five most highlyrecommended nonrandom sites, and the two nonrandom sites of particular interest to the park. 

2.4.3 Stations Selected Within MISS 

The GLKN large rivers monitoring program faces budget constraints, due primarily to the higher 

sampling frequency required by the inherent variability of the resource and the geographic extent 

of the SACN park unit. Fortunately, MISS lies within an urban metropolitan area and therefore is 

heavily monitored by regulatory agencies. All of these data should be available on-line (via the 

Internet) and data acquisition should not require formal, contractual agreements. 

Statistical power analysis was conducted to determine the sample size (number of random sites) 

needed to detect 20% change at 80% power (Table 9). Based on the sample size analysis of two 

out of four segments of MISS (Table 9), as many as 1 - 16 sites/segment (4 - 64 total) would be 

required to detect 20% change within each segment. These high numbers are not feasible; NPSGLKN cannot afford to monitor the MISS park unit with randomly-selected sites in each 

segment. However, nonrandomly-selected sites could be useful within MISS to fill spatial gaps 

in the existing monitoring of other agencies. The Great Lakes Network has determined that 

adding five monitoring stations to these on-going efforts will substantially close gaps in the 

existing monitoring programs. Individual stations will be analyzed for temporal trends; although 

this method is not as valid as that determined from a population trend, a consistent pattern in the 

trends could suggest a temporal trend for the entire corridor. In addition, the downstream 

sequence of stations will be analyzed for spatial trends. 

One possible monitoring approach could include monitoring sites at the upstream and 

downstream ends of MISS, to assess the water quality inputs to and outputs from the park unit. 

The upstream end of MISS is located at the confluence of the Mississippi River with the Crow 

River, and a monitoring station could be sited within the Mississippi River immediately above 

the confluence. However, the downstream end of MISS is below the confluence of the 

Mississippi and St. Croix Rivers, both of which are major drainage basins, and it requires several 

river miles before these two waters are adequately mixed. Attempting to sample at the 

downstream end of MISS would require a complex sampling method, where samples collected 

from the river’s cross-section would be weighted according to the flow volume of the crosssection. In the long run, the results would be a function of the relative flow volumes of the St. 

Croix and Mississippi Rivers. This information could more readily, and perhaps accurately, be 

acquired by analyzing St. Croix and Mississippi river water quality data using geochemical 

mixing software. 
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Figure 9. Monitoring stations within SACN, showing locations of six randomly-selected 

stations within the Upper (St. Croix and Namekagon Rivers) and Lower (Lake St. Croix) 

portions of the park unit and seven nonrandomly-selected stations. 

 
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Table 9. Within Miss, the 26-year mean values of the annual mean and coefficient of variation 

(CV, %), and the predicted sample size (number of sites) required to detect a 20% change at 80% 

power, based on the annual means (1980 - 2005) of four water quality variables: pH (standard 

units), dissolved oxygen (DO, mg/L), total phosphorus (TP, mg/L), and nitrogen oxides (NOx-N, 

mg/L). Two-tailed significance level α2 = 5%. 

River Segment Statistic pH DO TP NOx-N 

MISS 878-845 Mean 8.06 10.50 0.103 0.73 

(n = 2) CV (%) 0.7 7 13 25 

Sample size 1 4 7 16 

MISS 836-813 Mean 7.97 9.78 0.228 2.28 

(n = 3) CV (%) 0.5 3 8 4 

Sample size 1 3 4 3 

MISS 878-807 Mean 8.01 10.07 0.175 1.71 

(n = 6) CV (%) 0.9 6 38 47 

 Sample size 1 3 28 42 

In addition to a new monitoring site at the upstream end of MISS, sites could be added to fill 

spatial gaps between the monitoring stations of other agencies. In particular, 1) Spring Lake, 

between river mile 820 and 825, which has historical monitoring data, 2) the portion of MISS 

above river mile 848, along which significant water quality changes occur from undetermined 

sources (Johnson and Schellhaass, MCES, personal communication). By filling these spatial gaps 

in existing monitoring networks, GLKN will achieve a more accurate assessment of the water 

quality trends within the park unit. Potential locations of nonrandomly-selected monitoring 

stations are listed below, including the reason for possible inclusion. 

Selected MISS monitoring locations (Figure 10), given as river miles on the upper Mississippi 

(UM) River, and reason for inclusion: 

1) UM880 – Top of MISS, above confluence with Crow River, to assess incoming water 

quality 

2) UM868 – Above Coon Rapids Dam (easy access), incorporates upstream point sources, 

coordinates with riverine diatom monitoring 

3) UM862 – Metropolitan Council Environmental Services monitors weekly for limited 

variables; will monitor for additional variables 

4) UM852 – Top of Pool 1, above Lock & Dam #1, incorporates upstream point sources, 

coordinates with riverine diatom monitoring 

5) UM822 – Spring Lake, historically monitored, coordinates with riverine diatom 

monitoring 
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In summary, Table 10 lists the number of each station type (random or nonrandom) and the total 

number of monitoring stations selected for each park unit. All site locations have been fieldverified for representativeness and accessibility. 

Figure 10. Locations of the five nonrandomly-selected monitoring stations in MISS. 

Table 10. Number of randomly-selected and nonrandomly-selected monitoring stations in the 

Upper SACN, Lower SACN, and MISS park units. 

Station Type Upper 

SACN 

Lower 

SACN MISS 

Random 3 3 0 

Nonrandom 7 5 

TOTAL 13 5 
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2.5 Frequency and Timing of Sampling 

River systems respond dynamically to runoff and require more frequent sampling than lakes to 

define the average water quality conditions for a given year. However, autocorrelation can 

become important at high monitoring frequencies (e.g., weekly or more frequent). For most lotic 

water quality monitoring programs, year-to-year variations in the mean are assumed to be 

serially independent. 

The spreadsheet-based power analysis software LRSD-1.0 (Walker 1988) includes sensitivity 

analysis of sampling frequency. The effects of serial correlation (date-to-date within a given 

year) on the precision of annual and long-term means are considered using the “effective number 

of samples” concept. Autocorrelation reduces the effective number of samples for calculating the 

annual mean. The results of the sampling frequency sensitivity analysis based on a nine-month 

sampling season, using LRSD-1.0, for dissolved oxygen and total phosphorus are shown in Table 

11, listed in terms of the number of monitoring years required to detect 20% change at 80% 

power. The higher sampling frequencies require fewer monitoring years to detect a given level of 

change. The most cost-effective sampling frequency is biweekly (i.e., every-other week) 

sampling; however, monthly sampling has been selected at half the budget cost. This sampling 

frequency would not be sufficient to, for example, conduct storm-loading analysis, but is 

sufficient to meet the goal of the protocol to determine mean annual concentrations. 

In the upper midwestern United States, even the larger rivers freeze over during the winter 

months. Flow rates under the ice are low and water chemistry changes less than during other 

times of the year, although low oxygen levels can occur in rivers sealed by ice. Sampling an icecovered river can be difficult and dangerous where there is no bridge crossing over the 

monitoring station. Therefore, samples will be collected monthly only during the open water 

season, which is usually March through November, monitoring spring, summer, and autumn 

flows. The core water quality suite (dissolved oxygen, temperature, specific conductance, pH, 

flow, and clarity), nutrients (total phosphorus, total nitrogen, nitrite+nitrate-nitrogen, 

ammonium-nitrogen), total chlorophyll-a, and total suspended solids will be monitored monthly, 

while alkalinity, major ions (chloride, sulfate, calcium, sodium, potassium, and magnesium), 

dissolved organic carbon, and dissolved silica, which generally tend to be less variable, will be 

monitored quarterly. Randomly-selected and nonrandomly-selected stations in each park unit 

will be sampled at the same frequency, that is, during each sampling period. The current large 

river monitoring plan is to sample from one park unit each year, alternating between SACN and 

MISS. Quarterly sampling may be conducted in off-years, depending on perceived need and 

budget. Table 12 summarizes the large rivers sampling frequency and sampling return period in a 

panel array. Eventually, we will coordinate large river sampling events with other vital signs 

monitoring projects, such as aquatic biota. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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Table 11. Sampling frequency sensitivity analysis: number of monitoring years required to detect 

20% change at 80% power. LRSD-1.0 power analysis based on historical variability of dissolved 

oxygen and total phosphorus at two locations: on the upper St. Croix River (Danbury, 

Wisconsin) and the lower St. Croix River (Hudson, Wisconsin). 

Number of Monitoring Years Required 

Dissolved Oxygen Total Phosphorus Sampling 

Frequency 

Danbury, WI Hudson, WI Danbury, WI Hudson, WI 

Annual 10 25 >100 >100 

Bimonthly 2 3 >100 100 

Monthly 1 2 50 20 

Biweekly 1 2 25 10 

Weekly 1 1 20 10 

Semiweekly 1 1 20 10 

Table 12. Panel array of sampling frequency and return period for the large river parks, SACN 

and MISS. M=monthly sampling for nine months, March through November, Q=quarterly 

sampling April, July, and October. 

Monitoring Year Park Unit WQ Variables 1 2 3 4 

MISS Core suite M M 

 Nutrients M M 

 Total chlorophyll-a M M 

 TSS M M 

 Major ions Q Q 

 Alkalinity Q Q 

 DOC Q Q 

SiO2 Q Q 

SACN Core suite M M 

 Nutrients M M 

 Total chlorophyll-a M M 

 TSS M M 

 Major ions Q Q 

 Alkalinity Q Q 

 DOC Q Q 

 SiO2 Q Q 

TSS = total suspended solids 

DOC = dissolved organic carbon 

SiO2 = dissolved silica 
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2.6 Level of Change that can be Detected by Proposed Sampling Design 

2.6.1 Minimum Detectable Change 

Using the parameter values of the proposed randomly-selected sampling design for SACN (given 

mean and standard deviation, n = 3, α = 5%, 1-β = 80%) the on-line statistical power calculator 

(http:// calculators. stat.ucla.edu/ powercalc/ normal/ n-1/) resulted in the smallest value of the mean 

under the alternative hypothesis, μA, that would not reject the null hypothesis. In other words, it 

yielded the value of the minimum detectable change, or effect size, of the proposed sampling 

design (Table 13). The mean effect size is expected to be less than 10% for pH, less than 20% for 

dissolved oxygen, and about 100% for total phosphorus. Of the three water quality variables, 

only total phosphorus exceeded the goal of 20% minimum detectable change. 

Table 13. Within the upper and lower portions of the SACN park unit: the 30-year minimum, 

mean, and maximum values of the annual mean and coefficient of variation (CV, %), and 

minimum detectable change (effect size, %) for proposed sampling design (n = 3) at 80% power, 

based on the annual means (1974 - 2003) of three water quality variables: pH (standard units), 

dissolved oxygen (DO, mg/L), and total phosphorus (TP, mg/L). Two-tailed significance level α2

= 5%. 

 Upper St. Croix Lower St. Croix 

 Statistic pH DO TP pH DO TP 

Min Value Mean 6.85 8.32 0.018 7.42 8.45 0.036 

 CV (%) 0.2 1 3 0.04 2 1 

Effect size (%) 1 3 15 1 7 3 

Mean Value Mean 7.55 9.55 0.041 7.7 9.48 0.057 

 CV (%) 2 5 34 0.6 7 24 

Effect size (%) 7 16 104 2 21 74 

Max Value Mean 8.20 11.33 0.071 8.14 11.77 0.094 

 CV (%) 9 12 95 3 21 98 

Effect size (%) 28 38 296 8 66 300 

2.6.2 Minimum Duration of Monitoring Effort 

The software program TRENDS (http://swfsc.nmfs.noaa.gov/PRD/software/ Trends.html), 

shown in Figure 11, is designed to carry out a power analysis of linear regression, particularly in 

the context of monitoring populations in wildlife studies (Gerrodette 1987). TRENDS 

summarizes the power analysis in 5 parameters: duration of study, rate of change, precision of 

estimates (coefficient of variation), alpha (type 1 error rate), and power (1-β, where β is the type 

2 error rate). Based on the observed variation in historical monitoring data for the St. Croix 

River, TRENDS was used to determine the minimum number of monitoring years required to 

detect 20% change at 80% power (Table 14). The program would not accept CV < 0.01 (duration 

= 4 years) or CV > 0.13 (duration = 44 years). Therefore, all the values in Table 14 fall between 

4 and 44 years minimum duration of monitoring to detect 20% change. Of the three water quality 

variables, pH required only 1 or 2 monitoring years, dissolved oxygen fell within the range of 5-
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15 monitoring years, and the variations observed in total phosphorus were beyond the ability of 

TRENDS to estimate minimum duration of monitoring. 

Figure 11. Screen snap-shot of TRENDS statistical power analysis software. 

2.7 Expectation of Improvement in Post-Hoc Statistical Power 

It is expected that the post-hoc statistical power of the proposed sampling design, after several 

years of sampling for the large rivers protocol, will show substantial improvement over the 

results from the power analysis of the available historical data. The primary reason for this 

expectation is protocol consistency: in the sampling time of day and collection methods, in the 

processing methods, and in the analytical laboratory and laboratory methods. In a post-hoc 

analysis, the numbers given in the preceding power analysis tables of this chapter should be 

improved, but the degree of improvement cannot be anticipated. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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Table 14. Within the upper and lower portions of the SACN park unit: the 30-year minimum, 

mean, and maximum values of the annual mean and coefficient of variation (CV, %), and 

number of years required to detect 20% change at 80% power, based on the annual means (1974-

2003) of three water quality variables: pH (standard units), dissolved oxygen (DO, mg/L), and 

total phosphorus (TP, mg/L). Two-tailed significance level α2 = 5%. 

 Upper St. Croix Lower St. Croix 

 Statistic pH DO TP pH DO TP 

Min Value Mean 6.85 8.32 0.018 7.42 8.45 0.036 

 CV (%) 0.2 1 3 0.04 2 1 

 Years <4 4 5 <4 4 5 

Mean Value Mean 7.55 9.55 0.041 7.7 9.48 0.057 

 CV (%) 2 5 34 0.6 7 24 

 Years 4 8 > 44 < 4 13 > 44 

Max Value Mean 8.20 11.33 0.071 8.14 11.77 0.094 

 CV (%) 9 12 95 3 21 98 

 Years 5 > 44 > 44 5 > 44 > 44 
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3.0 Sampling Methods 

This section summarizes the information presented in greater detail in the standard operating 

procedures (SOPs) #1 (Pre-season Preparation), #6 (Field Measurements and Water Sample 

Collection), #7 (Processing Water Samples and Analytical Laboratory Requirements), and #11 

(Post-season Procedures). Refer to the SOPs for more information. In addition, this section ends 

with an overview of quality assurance and quality control (QA/QC) procedures, which pertain to 

all aspects of sampling. The details of QA/QC are presented in SOP #12. 

3.1 Field Season Preparations 

All details of field work need to be planned well in advance. Checklists help ensure that 

personnel, equipment, and supplies will be prepared in a timely and orderly manner. Table 15 

summarizes which of the SOPs contain key checklists of equipment and supplies for water 

sampling. Field personnel should check the inventory of equipment and supplies against these 

lists to verify that no necessary equipment or supply is missing. All equipment, meters, and 

probes should be checked to verify that they are functioning properly. If needed, replacement 

equipment or supplies should be ordered well in advance of the onset of sampling, to allow time 

for inspection, pilot-testing, and calibration of replacements. 

Table 15. Checklists of equipment and supplies for monitoring water quality of large rivers. 

Checklist Location 

Safety equipment and supplies SOP #2 

Decontamination equipment and supplies SOP #5 

Field equipment and supplies SOP #6 

Laboratory equipment and supplies SOP #7 

Table 16 provides general guidance for activities conducted prior to the field season. Additional 

considerations are as follows: 

1) Copies of field information on waterproof paper should be kept in two types of 3-ring 

binders: an office binder and field binders. The office binder should contain reference 

information relevant to general field sampling procedures with tabs identifying each 

procedure for easy access during field work, including QA/QC reminders, a copy of the 

protocol narrative and all SOPs, copies of equipment instructions and troubleshooting; 

extra field forms, material safety data sheets for field supplies that contain hazardous 

chemicals or materials, and analytical service request and chain of custody forms. Field 

binders should contain reference information specific to each sampling station, including 

complete description of and directions to the monitoring site, location coordinates, maps, 

photos, copies of previous field forms; summaries of sampling and QA/QC procedures; 

and data tables summarizing all previous measurements of field variables and analytical 

laboratory results. Both office binder and field binders should be thoroughly reviewed 

before the season begins. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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Table16. Checklist of preparation for field season, approximate date of activity, and person 

responsible. 

2) Field personnel should be adequately experienced or trained in using field and water 

quality sampling equipment. This experience is best obtained through a combination of 

classroom and hands-on training while pilot-testing equipment at a nearby waterbody. 

√ Activity Approximate Date Responsible Person 

Prepare calendar of planned field 

trips Before Feb. 1 Project manager 

Review sampling methods Jan. - Feb. Project manager 

Review checklists of equipment 

and supplies required Jan. - Feb. Crew leader 

Charge/replace batteries as needed Feb. and prior to each 

sampling round Field personnel 

Clean and test equipment, repair or 

replace as needed 

Jan. - Feb. and prior to each 

sampling day Project manager or crew leader 

Prepare equipment blanks Feb. Project manager or crew leader 

Check expiration dates of stock 

reagents and calibration standards Feb. Crew leader 

Contract for lab analyses Jan. - Feb. Project manager 

Prepare list of items to be ordered; 

order supplies Jan. - Feb. Crew leader 

Train field personnel Jan. - Feb. Project manager 

Obtain permission for site access, 

if necessary Feb. Project manager 

Confirm current research and 

collection permits Jan. - Feb. Project manager 

Check field vehicle for safety 

equipment and supplies 

Feb. and prior to each 

sampling day Crew leader 

Update site binders Jan. - Feb. Project manager or crew leader 

Prepare headers on field data 

forms, chain of custody forms, 

analytical service request forms; 

bottle labels 

Prior to each sampling round Crew leader 

Review sample collection, 

processing and documentation 

information 

Feb. 

(Refer to SOPs #6 & #7) 

Project manager and all crew 

personnel 

Notify contract analytical 

laboratory of planned sample 

shipments 

Prior to each sampling round 

and day of shipment Crew leader 

Make travel reservations and 

arrangements as needed 

Feb. and prior to each 

sampling round 

Project manager and crew 

leader 

Provide supervisor with field trip 

and check-in schedule Prior to each sampling round Crew leader 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

37 

Personnel should be familiar with the instruction manuals, particularly with regard to 

calibration and maintenance procedures. 

3) Meters and probes should undergo appropriate annual, weekly, and daily calibration. (See 

Table 21 for calibration frequencies and acceptance criteria.) 

4) Conduct field reconnaissance, if necessary. 

5) Pack all field gear to minimize shock and vibration during transport. Pack gear into 

organized and labeled boxes or cartons, to facilitate inventory and management of 

supplies. 

6) Inspect motorized field vehicles to verify that they are tuned-up and working properly. 

Ensure that vehicles meet space, power, and towing requirements. 

3.2 Details of Taking Field Measurements and Collecting Samples 

3.2.1 Sequence of Activities During Field Workday 

This subsection gives a general overview of all sampling tasks and detailed descriptions of 

particular tasks. Following is the sequence of activities during any given field day: 

1) Review checklist of field gear. 

2) Create a new field form for each monitoring station, printed on waterproof paper. 

3) Prepare sample bottles and labels in advance. 

4) Conduct daily calibration of appropriate meters and probes. 

5) Inspect motorized field vehicles at the beginning of every field day, including all safety 

and directional lights, oil, gasoline, and tire air pressure levels. 

6) Drive to monitoring site. If sampling from a bridge, set out traffic safety cones. If 

sampling by boat, load boat with sampling gear, launch boat, and navigate to monitoring 

site. Set up a clean work space on the boat for sampling. 

7) Refer to description of monitoring station location, directions, and photos to verify 

correct location. Verify coordinates on GPS unit. 

8) Measure field water quality variables and conduct sampling per SOP #6. 

9) Be sure that all samples are correctly labeled and preserved on ice. 

10) Clean sampling equipment per SOP #6. Rinse sensors with deionized water and perform 

calibration re-checks, as detailed in SOP #6. 

11) At selected sites, record stage reading and measure discharge per SOP #4. 

12) Verify that field form is completely filled out, and initial the form. 

13) Upon return to shore, inspect boat, trailer, and all equipment that has come into contact 

with the water for invasive species. Follow procedures for decontamination of equipment 

per SOP #5. 

14) If sampling from more than one monitoring station in a day, go back to step 7. 

15) Return to office or park laboratory. 

16) Conduct sample processing per SOP #7. Refrigerate or freeze samples, as required. 

Conduct in-house laboratory work and package samples for sending to contract analytical 

laboratory. 

17) Enter data into NPSTORET as soon as feasible after collecting field data and receiving 

laboratory results. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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3.2.2 Arrival at Monitoring Site - Recording Field Information 

Waterproof field forms should be prepared ahead of time, labeled with the project and station 

IDs. Field data forms are used to record the physical and chemical water quality variables 

measured at the time of sample collection. In addition to recording the field variables, any 

samples collected for laboratory analyses must be so indicated. Documentation should include 

calibration data for each instrument, field conditions at the time of sample collection, visual 

observations, and other information that might prove useful in interpreting these data in the 

future. 

While at each monitoring site, the information recorded on field datan forms should include: 

• Date and day of week 

• Time of arrival 

• Names of field team members 

• GPS coordinates, to verify location 

• Current weather (air temperature, sky conditions, and wind speed and direction) and 

relevant notes about recent weather (storms or drought) 

• Observations of water quality conditions 

• Description of any photographs taken 

• Multiparameter meter (model), calibration data, and field measurements of core suite 

variables 

• List of sample IDs and collection times for advanced suite variables or quality assurance 

samples 

• Whether any samples were not collected, and reason 

• Flow discharge information and measurements (on separate form) 

• Any other required metadata for STORET data entry 

• Time of departure 

All entries should be made clearly. If an incorrect entry is made, a single heavy line should be 

drawn through the incorrect entry and the correction made. All corrections should be initialed 

and dated. The completed field forms will be maintained in chronological order by station, 

copied into site binders and the originals maintained on file indefinitely. Field data are reviewed 

annually by network personnel (see SOP #8, Data Entry and Management, for details). 

Observations of Water Quality Conditions: Upon arrival at the monitoring station, record visual 

observations of water quality conditions that will be useful in interpreting water quality data. To 

be consistent and to help orient others to the location of observations, the convention left 

bank/right bank is used. Left bank is defined as the bank to the left of the observer when facing 

downstream, and the right bank is to the right of the observer when facing downstream. 

• Water appearance — General observations of water may include: color, unusual amount 

of suspended matter, debris, or foam. 

• Biological activity — Excessive macrophyte, phytoplankton, or periphyton growth. The 

observation of water color and excessive algal growth is important in explaining high 

chlorophyll-a values. Other observations to note include fish, birds, or spawning fish. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

39 

• Unusual odors — Examples include hydrogen sulfide, mustiness, sewage, petroleum, 

chemicals, and chlorine. 

• Watershed or instream activities — Activities or events that may be impacting water 

quality; for example, bridge construction, shoreline mowing, dredging, or livestock 

watering upstream. 

3.2.3 Measurement of Field Water Quality Variables 

Electronic sensors must meet the quality control specifications for resolution and accuracy listed 

in Table 17. Probes must be submerged and allowed to stabilize prior to recording any readings 

(see stabilization criteria in Table 17). 

After disturbances from the boat anchor have cleared, take field measurements of the core suite 

of field variables on the upstream side of the boat; methods are listed in Table 18 and detailed in 

SOP #6 and specific multiprobe instrument manufacturers’ instruction manuals. Measurements 

should be made in the center of channelized flow, in a vertical profile of the water column. 

Replicate at least 10% of readings, with the replicate taken immediately following the original 

reading; values should agree within 10% or the stabilization criteria in Table 17, whichever is 

larger. Use the transparency tube to measure the clarity of a surface sample. 

Table 17. Typical sensor performance specifications for field instruments (Penoyer 2003). 

* Resolution specifications are supplied by the manufacturers of the measuring meters. They are not necessarily closely related to 

real-world (outdoor) precision or bias, and are sometimes more related to the number of significant figures reported rather than 

how accurate the extra significant figures are. This is why we will control measurement sensitivity in the actual outdoor 

measuring environment at least once a year by calculating alternative measurement sensitivity (AMS; see Irwin 2006 for more 

details on AMS). 

Sensor Expected 

Range 

Reporting 

Resolution* Estimated Bias Stabilization Criteria 

Temperature -5 to 45 °C 0.01 °C ±0.15 °C Thermistor: ± 0.2 °C 

Glass: ± 0.5 °C 

Specific 

Conductivity (SC25) 

0 to 2000 

 μS/cm 

μS/cm 

(range 

dependent) 

±0.5% of reading + 1 

μS/cm 

≤100 μS/cm: ± 5% 

>100 μS/cm: ± 3% 

pH 1 to 14 units 0.01 unit ±0.2 units ± 0.1 standard unit 

Dissolved Oxygen 

(Conc.) 0 to 50 mg/L 0.01 mg/L 

0 to 20 mg/L: ±0.2 

mg/L 

20 to 50 mg/L: ±0.6 

mg/L 

± 0.3 mg/L 

Dissolved Oxygen 

(% sat.) 0-200% 0.1% ~ ±2 % ± 2 % 

Depth – Z (pressure 

sensor) 0 - > 100 m 0.1 m ~ 0.1 m 0.1 m 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

40 

Table 18. Core suite of field variables and required methods for in situ measurements. 

Field Variable Method 

Temperature (°C) EPA 170.1 

pH EPA 150.1 

Specific conductivity (μS/cm) EPA 120.1 

Dissolved oxygen (mg/L) EPA 360.1 

Clarity (cm) Transparency tube 

3.2.4 Sample Collection 

Collect samples on the upstream side of the boat from the center of channelized flow as per SOP 

#6. Table 19 summarizes the variety of methods, detection limits, preservation techniques, and 

holding times for water samples addressed by this protocol. Methods conform to those used by 

Minnesota, Wisconsin, and Michigan for state certification of environmental laboratories 

involved in Clean Water Act or drinking water sample analysis (MDH 2005; WSLH 2003; 

MDEQ 2005). They are also used by EPA-funded research projects of natural waters in the upper 

midwestern U.S. Refer to SOP #6 for additional details regarding sample collection and 

preservation. 

Always keep the following in mind: 

• On the field form, record sample date and time, sample ID and type (e.g., alkalinity), and 

whether quality control replicate samples were collected. 

• Sample bottles should be clearly labeled with the sample ID, station name, date and time 

of collection, and acid preservation method if applicable. 

• To ensure the integrity of the sample, be aware of possible sources of contamination. 

Contamination introduced during sample collection (and processing) is additive and 

usually is substantially greater than contamination introduced elsewhere in the sample 

handling and analysis (Wilde et al. 1999). 

• Use appropriate procedures and quality assurance measures that ensure sample 

representativeness and integrity and that meet study criteria. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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Table 19. Example range of analytical methods, method detection limits (MDLs), containers, 

preservation methods, and holding times. 

Analyte Analytical 

Note 1 Method # Det. Limit Vol. (ml) Filter Preservation 

Sample 

Bottle 

Note 2 

Hold Time 

Titrimetry 310.1 EPA-NERL 10 mg/L 4oC 14 days Alkalinity Spec. auto. 310.2 EPA-NERL 10 mg/L 4o

C 14 days 

 Titrimetry NFM USGS-OWQ 0.01 meg/L Note 4 None none 

ICP 3120B APHA 10 ug/L Note 3 pH<2 HNO3 P or G 6 mos 

Titrimetry 215.2 EPA-NERL 0.5 mg/L Note 3 4o Calcium C 6 mos 

FAA I-3152 USGS-NWQL 0.1 mg/L 250 Note 3 pH<2 HNO3 P 180 day 

IC 300.0 EPA-NERL 0.02 mg/L 4o

C P or G 28 day 

Colorimetry 325.2 EPA-NERL 1 mg/L 4o Chloride C 28 day 

Titrimetry 4500-Cl APHA 0.15 mg/L 100 4o

C P or G 28 day 

Chlorophyll-a Spect. 10200 APHA 2 ug/L < 1 L Note 4 Freeze filter P 30day 

Spect. 110.2 EPA-NERL 5 Pt units Note 5 4oC G 48 hours Color Vis. Comp. I-1250 USGS-NWQL 1 Pt-co 250 Note 5 4o

C P 30 days 

Spect. 415.3 EPA 0.018 mg/L 125 Note 3 pH<4 H2SO4 G 28 days DOC Spect. 0-1122-92 USGS 0.1 mg/L 4o

C AG 

ICP 3120B APHA 0.3 mg/L Note 3 pH<2 HNO3 P or G 6 mos K FAA 3111B APHA 5 ug/L Note 3 pH<2 HNO3 P or G 6 mos 

ICP 3120B APHA 20 ug/L Note 3 pH<2 HNO3 P or G 6 mos Mg FAA 3111B APHA 0.5 ug/L Note 3 pH<2 HNO3 P or G 6 mos 

ICP 3120B APHA 30 ug/L Note 3 pH<2 HNO3 P or G 6 mos Na FAA 3111B APHA 2 ug/L Note 3 pH<2 HNO3 P or G 6 mos 

Selective elec. 4500-NH3E 0.08 mg/L 4o

C/pH2,0oC 24h/28d 

NH4-N Colorimetry 350.2 EPA-NERL 0.08 mg/L pH<4 H2SO4 28 day 

Titrimetry 4500-NH3 APHA 5 mg/L 4o

C/pH2,0oC 24h/28d 

ICP 3120B APHA 20 ug/L Note 3 pH<2 HNO3 P or G 6 mos 

Spect. 4500- SiO2 D APHA 0.04 mg/L Note 3 No, 4o SiO2 C P 28 days 

FIA-Spect. 4500- SiO2 F APHA 0.78 ug/L Note 3 No, 4o

C P 28 days 

TSS Gravimetric I-3765 USGS-NWQL 1 mg/L 250-

500 Note 4 4o

C filter P NA 

IC 4110C APHA 75 ug/L Note 3 pH<4 H2SO4 P or G 

SO4 CIE-UV D6508 ASTM 0.1 mg/L Note 3 pH<4 H2SO4 ASAP 

Spect. 37512 EPA-NERL 0.5 mg/L Note 3 pH<4 H2SO4 P or G 28 days 

Spect. I-2606 USGS-NWQL 0.001 mg/L 125 MgCl 4o

C BrownP 30 days 

Alkaline P USGS 2003 0.01 mg/L 120 Note 6 4oC /H2SO4 TP 48 h/30d 

ICP 200.7 EPA-NERL 60 ug/L pH<2 HNO3 P 6 mos 

Alkaline P USGS 2003 0.03 mg/L 120 Note 6 4o

C /H2SO4 48 h/30d 

Titrimetry 4500-N 0-100 mg/L 4o TN C AG 7 days 

Combustion 440.0 EPA-NERL 0.1 mg/L Filter 100 day 

Source: National Environmental Methods Inventory website (NEMI 2006) 

This list is not an endorsement of any particular method or laboratory for any particular analyte. Rather it is to be used as a

reference for the range of analytical methods available for each analyte. There are surface water conditions (pH, turbidity, other 

elements) that make a particular method unsuitable for a particular situation. As GLKN is monitoring surface water, the methods

listed were chosen as representative of the lower range of detection limits. 

Note 1. CIE-UV= capillary ion electrophoresis with UV detection, FAA = flame atomic absorption, FIA = flow injection 

analysis, IC= ion chromatography, ICP = inductively coupled plasma, Spec. auto = spectroscopy with autoanalyzer 

Note 2. P = plastic (polypropylene), G=glass, AG=amber glass 

Note 3. 0.45μm membrane filter. Pre-filter for dissolved portion analysis. 

Note 4. 0.45μm glass fiber filter. 

Note 5. 0.45μm membrane filter or centrifuge is recommended to remove suspended solids that affect color, however some color 

will also be removed. 

Note 6. Patton, C.J. and J.R. Kryskalla. 2003. Evaluation of Alkaline Persulfate Digestion as an Alternative to Kjeldahl Digestion 

for Determination of Total and Dissolved Nitrogen and Phosphorus in Water .U.S. Geological Survey Water-Resources 

Investigations Report 03-4174.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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3.2.5 Measurement of Flow Stage and Discharge 

When appropriate, record stage reading and discharge measurements using a current meter. 

Record information on a separate field form (Field Discharge Measurements). 

3.2.6 Departure from Monitoring Site 

Before leaving the monitoring site, all field forms, discharge measurement forms, and sample 

labels must be reviewed for legibility, accuracy, and completeness. All flags must be explained 

in the comments section. Make sure the header information is complete on all forms. Record 

departure time on field form. After reviewing each form, initial the upper right corner of each 

page of the form. 

 

3.2.7 Upon Return to Shore 

Upon return to the shore, inspect and clean all equipment that has come in contact with river 

water according to SOP #5, Decontamination of Equipment to Remove Exotic Species. This 

effort limits the spread of nuisance species and prevents possible cross-contamination of 

samples. 

Return all equipment and supplies to the field vehicle and pack them for transport in labeled 

crates or boxes. Keep equipment and supplies organized so they can easily be inventoried using 

checklists. Properly dispose of any waste material. 

3.3 Post-Collection Sample Processing 

Upon return to the office or home base, prepare and ship sample bottles, conduct in-house 

laboratory work, clean and prepare equipment for storage, and enter data from field forms into 

NPSTORET. 

3.3.1 Shipping Samples to Contract Laboratory 

Samples should have been put on ice for preservation immediately after collection in the field. In 

addition, the laboratory should have been notified, prior to field work, of how many samples of 

what type and when to expect shipment. Check that the sample bottles are correctly labeled 

according to the protocols of the contract laboratory and that caps are securely tightened. 

Complete the Analytical Services Request (ASR) form and/or the Chain-of-Custody (COC) form 

provided by the laboratory, recording the laboratory sample identification numbers for each 

sample type on the field form. Pack samples carefully in the shipping container according to 

laboratory protocols, to prevent bottle breakage, shipping container leakage, and sample 

degradation. 

3.3.2 In-House Laboratory Work 

If any of the water quality analyses are being done in-house (for example, alkalinity titrations or 

total suspended solid filtrations), conduct these procedures as soon as possible after returning 

from field work, ensuring that the maximum holding times for these variables are not exceeded. 

Upon return from the field, samples bottles should be refrigerated prior to analysis. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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3.3.3 Equipment Cleaning and Storage 

Clean all sample collection and storage containers and labware in a 0.1N HCl acid bath followed 

by deionized water rinses per SOP #7. Monitoring equipment should be cleaned and packed for 

storage. Keep equipment and supplies properly organized and labeled so they can easily be 

inventoried using the checklists. 

3.3.4 Data Entry and Management 

Enter data into appropriate spreadsheets and databases as soon as possible to minimize error. 

Refer to the instrument manufacturer’s instruction manual for details on downloading data from 

field dataloggers. Field and laboratory data should be entered into the GLKN database as soon as 

possible for transfer to NPSTORET, per SOP #8. Update the data in the field file to include the 

latest field measurements. 

3.4 End of Field Season Procedures 

When sensor probes are to be stored for extended periods of time, thoroughly clean sensors, 

remove batteries, and store sonde according to specific instructions in SOP #11 and 

manufacturer’s manual. Store calibration standards and electrolyte solutions in a temperaturecontrolled environment. Ensure containers are dated upon receipt and upon opening. 

Commercially-purchased calibration standards come with an expiration date that must be 

observed. Staff can conduct these annual procedures after the end of the field season. 

3.5 Quality Assurance and Quality Control Pertaining to Sampling Methods 

The objective of quality assurance/quality control (QA/QC) is to ensure that the data generated 

by a project are meaningful, representative, complete, precise, accurate, comparable, and 

scientifically defensible (O’Ney 2005). It is a broad management concept requiring the complete 

integration of field and laboratory procedures for sample collection and analysis. The QA/QC 

procedures that pertain to sample collection and processing are focused on: 1) ensuring that any 

given field or laboratory measurement accurately represents the water resource at the time the 

sample was collected, 2) ensuring that water quality data are comparable across all sampling 

dates, and 3) verifying that no contamination has been introduced to the sample at any time. 

These activities range from instrument calibration, to sampling from the streamflow midpoint, to 

specification of field methods and laboratory detection limits, to analysis of sample blanks and 

spikes. Table 20 summarizes the QA/QC procedures pertaining to sampling methods that will be 

followed by this protocol. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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Table 20. Summary of QA/QC procedures pertaining to sampling methods. 

Procedure Description/Reason 

Instrument calibration logs 

Each instrument must have a logbook. All calibration results and 

maintenance activities must be recorded in the log. Calibration schedule 

must be observed, using fresh calibration standards. 

Office binder 

This binder will contain a complete copy of the protocol and all SOPs, 

Material Safety Data Sheets, analytical service request and chain of 

custody forms. 

Field binders 

This binder will contain directions for how to get to sampling site, GPS 

coordinates for verification of correct sampling location, table of previous 

field measurements to compare with new measurements, summaries of 

sampling and QA/QC procedures, discharge rating curve to verify new 

stage readings. 

Field forms Photocopies of field forms are placed in site binders and original field 

forms must be kept on file at a secure location indefinitely. 

Field instrument methods 

Consistent measurement methods and detection limits are required. Refer 

to SOP #6 for field methods and manufacturer’s instruction manuals for 

troubleshooting. 

Sample preservation and 

minimum holding time 

Transport and store water quality samples in the cold and dark in order to 

maintain sample parameter concentrations as close to sampling conditions 

as possible. Send samples to analytical lab in a timely manner so as to 

adhere to holding times. 

Chain-of-custody 

A chain of custody includes not only the form, but all references to the 

sample in any form, and documents the possession of the samples from the 

time they were collected until the sample analytical results are received. 

Laboratory methods Require consistent analytical methods and detection limits 

One important aspect in the accuracy and precision of a water quality monitoring program is the 

correct selection of field instruments and their subsequent calibration and maintenance schedule. 

Table 17, above, lists typical field sensor performance specifications that are expected from 

monitoring equipment used for this protocol. Table 21 summarizes the ideal calibration 

frequency and minimum acceptance criteria for these probes. The reality of logistical constraints 

at back country sites may preclude calibration and checks of calibration at the ideal frequency. 

Maintain calibration logs for multi-parameter sondes to document the frequency of calibration 

and calibration checks. Ensure calibration standards are not used beyond expiration dates. Refer 

to SOP #6 for guidelines on potential field measurement problems. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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Table 21. Ideal calibration frequencies and acceptance criteria for field instruments. 

Parameter USEPA 

Method 

Minimum Calibration Frequency and 

QC checks 

Acceptance 

Criteria Corrective Actions 

Temperature 

thermometer 

or thermistor 

170.1 

Annually, 2-point check with NIST 

thermometer 

 ±1.0 oC 

Re-test with a different 

thermometer; repeat 

measurement 

Specific 

Conductance 

(SC25) 

120.1 

Daily, prior to field mobilization; 

calibration check prior to each round 

of sampling; 10% of the readings taken 

each day must be duplicated or a 

minimum of 1 reading if fewer than 10 

samples are read. 

±5% 

RPD 10% 

Re-test; check low battery 

indicator; use a different 

meter; use different 

standards; repeat 

measurement 

pH 150.1 

Daily, prior to field mobilization (two 

buffers should be selected that bracket 

the anticipated pH of the water body to 

be sampled with an independent third 

buffer selected to check instrument 

performance in that range); 

Calibration check w/ third buffer prior 

to each round of sampling 

10% of the readings taken each day 

must be duplicated or a minimum of 1 

reading if fewer than 10 samples are 

read. 

±0.05 pH unit 

±0.1 pH unit 

RPD 10% 

Re-test; check low battery 

indicator; use different 

standards; repeat 

measurement; don’t move 

cords or cause 

friction/static 

 

Dissolved 

Oxygen 360.1 

Daily, prior to field mobilization; 

check at the field site if elevation or 

barometric pressure changed since 

calibration 

0.2 mg/L 

concentration 

or 

±10% 

saturation 

Re-enter altitude; re-test; 

check low battery indicator; 

check membrane for 

wrinkles, tears or air 

bubbles; replace 

membrane; use a different 

meter; repeat measurement; 

allow more time for 

stabilization 

Depth -- 

Daily, prior to field mobilization, 

check at the field site. Check annually 

against commercially purchased brass 

sash chain labeled every 0.5 m to 

ensure that it reads zero at the surface 

and varies <0.3 m for depths <10 m 

and no more than 2% for greater 

depths. 

±0.1 m 

Retest, check low battery 

indicator; repeat 

measurement; use with 

accurately calibrated line 

Transparency 

tube -- Transparency tubes have a 100 or 120 cm scale; ensure tube is clean 

±1.0 cm for 

transparency 

tube 

Marked lines 

(e.g., Secchi, 

Van Dorn) 

-- 

Check markings annually against brass 

sash chain. If lines are heated (for 

decontamination) check prior to each 

round of sampling. 

±1%, 0–10 m 

±2%, >10 m 

Re-mark line. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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The detection limits for water quality variables specified in Tables 17 and 19 are based on 

examination of historical data and the occurrence of dilute concentrations of water quality 

variables in natural waters. Many commercial laboratories do not routinely analyze samples 

using these lower detection limits, even if they have the proper instrumentation, because their 

primary work load is wastewater-related with much higher concentrations. Therefore, the process 

of selecting a contract analytical laboratory will include consideration of whether the lab has 

experience analyzing naturally dilute waters. 

We will conduct the following QA/QC routines: 

1) Collect equipment blanks prior to the field sampling, to ensure no extraneous sources of 

contamination are introduced into the samples. 

2) Collect duplicate water samples, at the rate of approximately 10%, so that the reported 

data are precise, or results of analyses are reproducible. 

3) Document the sensitivity of multiprobes through an estimation of the limits of detection 

known as alternative measurement sensitivity (AMS). 

4) Replicate multiprobe field measurements at the rate of approximately 10%. Calculate the 

relative percent difference to document precision of the multiprobe. 

5) Estimate systematic error/bias of the multiprobe through the use of reference solutions. 

 

Table 22 summarizes these QA/QC sample types and SOP #12 describes them in greater detail. 

Additional types of blanks (bottle, preservation, trip, or field) will be pursued if necessary to 

resolve problems. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

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Table 22. Summary of the types of QA/QC samples. 

Sample Type Field/Lab Definition Purpose 

Equipment 

blank 

Field 

& 

Lab 

A blank prepared by rinsing 

cleaned field equipment with 

deionized water, collecting the 

water in a sample, and analyzing 

the water 

Verify that field equipment cleaning 

and decontamination procedures are 

adequate, with no cross contamination 

between samples and no contamination 

due to collection 

Duplicate 

water sample Lab 

Two or more samples from one 

collection container for 

laboratory analysis 

Evaluate the precision and 

reproducibility of laboratory analysis 

Alternative 

measurement 

sensitivity 

Field 

A calculation of measurement 

uncertainty based on multiple 

measurements in the field with a 

multiprobe 

Document the sensitivity of the 

multiprobe 

Replicate 

multiprobe 

measurements 

Field 

A replicate reading of a 

parameter on the multiprobe 

taken immediately after the first 

reading 

Estimate the precision of multiprobe 

Check 

multiprobe 

against 

reference 

solutions 

Field 

& 

Lab 

Using multiprobe readings 

against known reference 

solutions to calculate relative 

percent difference between 

observed and expected readings 

Estimate systematic error/bias of 

multiprobe 

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4.0 Data Handling, Analysis, and Reporting 

4.1 Metadata Procedures 

Metadata allows potential data users to evaluate the quality and usefulness of the data based on 

an understanding of the complete process under which it was collected and maintained. In this 

respect, all of the protocol documentation, including standard operating procedures (SOPs), is 

part of a dataset’s metadata. A reference to the appropriate version of these documents is part of 

the metadata for any particular element of a dataset. Although perhaps obvious, all data must 

have an associated value for the date and time they were collected. 

Most of the remaining metadata will be recorded directly in the protocol-specific databases and 

tables. We will enter all required metadata for NPSTORET; the data and metadata will 

ultimately be moved to the EPA STORET database. 

For metadata associated with geospatial data, we will abide by Executive Order 12906, which 

mandates that every federal agency document all new geospatial data it collects or produces 

using the Federal Geographic Data Committee (FGDC) Content Standard for Digital Geospatial 

Metadata (CSDGM; www.fgdc.gov/metadata/contstan.html). All GIS data layers will be 

documented with applicable FGDC and NPS metadata standards. The Network will also generate 

FGDC-style metadata for non-spatial datasets that meet this standard, absent only the geospatialspecific elements. 

Although it is not required, we will make every effort to complete Biological Data Profiles 

(www.fgdc.gov/standards/status/sub5_2.html) for appropriate datasets and add associated 

metadata to the National Biological Information Infrastructure (NBII) Clearinghouse 

(www.nbii.gov/datainfo/metadata). 

For more details on the Great Lakes Network’s overall strategy for metadata generation, 

management, and distribution see chapter 8, Data Documentation, of GLKN’s Data Management 

Plan (Hart and Gafvert 2005) and the appendices of that document. 

4.2 Overview of Database Design 

The NPS -WRD has established a policy that all I&M water quality monitoring data will be 

made compatible with, and be uploaded to, the EPA’s STORET database. The WRD developed a 

Microsoft Access database tool, NPSTORET, which duplicates most of the data and table 

structures in EPA STORET, to facilitate easier movement of I&M networks’ water quality data 

into EPA STORET format. We will use NPSTORET as the primary data entry tool, and data 

transfer mechanism to WRD. 

To meet the data flow requirements of NPS-WRD, the Network’s version of NPSTORET will be 

able to export and import water quality data from the master version of STORET maintained by 

WRD. One of the primary methods GLKN uses for data distribution is the Vital Signs Internet 

Mapping Service (VSIMS) that allows users to explore and query monitoring data using spatial 

and non-spatial parameters. Network (GLKN) versions of NPSTORET are used to update a 

master version of STORET maintained by NPS WRD. The WRD master copy of STORET data 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

50 

is the data source that is used by the VSIMS to serve water quality data collected by GLKN and 

other I&M networks. 

The Great Lakes Network will maintain one master copy of NPSTORET at the Ashland office 

on a central server. This is the only copy of NPSTORET that can be used to export data to other 

locations. Additional copies of NPSTORET can be used by Network staff or cooperators, but 

they can only be used as a conduit for data entry and the importation of data to GLKN’s master 

version of NPSTORET. For analysis, the data from the master copy of NPSTORET must be 

used. 

4.3 Data Entry, Verification, and Editing 

Detailed instructions for the data entry procedures for this protocol are given in SOP #8, Data 

Entry and Management. As described in section 3, above, three general classes of water quality 

data are collected. The first is field observations and measurements that are recorded on data 

sheets in the field. These field sheets will be entered into a digital form in NPSTORET. The 

second class of data is the results of testing performed by contract analytical laboratories. An 

import routine will be created to bring in laboratory results and QA/QC procedures. The last 

class of water quality data is digital data that have been collected by multiprobe sondes and other 

field data loggers. Import routines will be used to enter these data into NPSTORET. 

Data verification starts with the QA/QC steps that are outlined in the SOPs associated with this 

protocol. If data being entered into NPSTORET do not pass a QA/QC test, NPSTORET prompts 

the user to make corrections and re-enter the data. Data that are outside the expected rate of 

change for a parameter based on previous records for that parameter will be flagged for further 

review by an expert. 

Quality assurance/quality control checks are performed as data are entered into NPSTORET and 

again when the data are transferred to WRD. The Network’s water quality data records are 

regarded as being in provisional status until they are returned to GLKN from WRD, or are 

accepted by WRD without changes after the final QA/QC steps. Only qualified users who have 

been trained and given edit permissions are allowed to edit data in NPSTORET. These 

procedures protect the integrity of the data and allow the history of each data record to be traced. 

4.4 Data Archival Procedures 

Data archiving serves two primary functions: it provides a source to retrieve a copy of any 

dataset when the primary dataset is lost or destroyed, and it provides a data record that is an 

essential part of the QA/QC process. The unedited files are the original data for digital data. The 

archival process of the printed data forms is described in SOP #8 of this protocol. 

The Network will create duplicate files of all digital data at the earliest opportunity. At least two 

complete copies of any water quality dataset are required by WRD, including digital replicas 

(scanned versions) of hard copy data sheets. Digital field data that are entered directly into a field 

computer or collected from a data logger will be backed up to a second medium at the earliest 

possibility. The data files on field computers and loggers must not be erased until the integrity of 

these data files are verified on the duplicate storage medium. 
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The Network’s master version of NPSTORET is maintained on a central server in the Ashland 

Office that is backed up daily, and backed up off-site weekly. Complete details of the GLKN 

Server archiving procedure are found in the Infrastructure chapter of GLKN’s Data Management 

Plan (Hart and Gafvert 2005); the general strategy for data archiving is also described in this plan 

and its appendices. 

4.5 Quality Assurance and Quality Control Pertaining to Data Management 

Quality assurance and quality control procedures are crucial during every step of data entry and 

data management. Details of such QA/QC regarding data management are provided in SOP #8 

and are summarized below in Table 23. 

4.6 Routine Data Summaries 

As mentioned above, flow directly influences values of most water-quality variables because 

many are expressed as concentrations (i.e., mass per volume). Consequently, because the 

purpose of water-quality monitoring is often to detect change in the level of the mass, 

independent of volume of water present, measured concentrations must have the effect of flow 

removed. Flow-adjusted concentrations are thus not subject to the confounding influence that 

variable flow rates can produce. In particular, one uses regression or a smoothing technique (e.g., 

LOWESS) to obtain residuals from a relationship of concentration vs. flow (on a log-log scale). 

Trend analysis is subsequently performed on the residuals, which are presumably detrended for 

flow. 

Brief characterizations of the data from each NPS unit that was sampled and the Network as a 

whole will be performed each year, after all QA/QC procedures have been completed. For each 

station sampled, these descriptive statistics will include mean, median, maximum and minimum 

values, skew, kurtosis, and measures of variability (e.g., CV, standard error, variance) for each 

water quality variable. Understanding of landscape-scale dynamics will be provided by analyses 

of variability among stations within the domain of interest (e.g., upper St. Croix River), 

following one of several approaches described in SOP #9, Data Analysis. 

Given the relevant legislation (e.g., Clean Water Act of 1972), it may be of interest to the 

individual NPS units and to other entities to assess the proportion of measurements during a time 

period or across a domain (at a single point in time) that exceed pre-determined thresholds. As 

with nearly all percentage data, arcsine transformations must be performed on the data before 

statistical analyses can be conducted. 
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Table 23. Summary of QA/QC procedures pertaining to data management. 

Procedure Description 

Instrument calibration logs Each instrument must have a calibration and maintenance 

logbook. 

Field forms 

Field forms are the only written record of field measurements. 

Place copies in site binders and keep originals on file 

indefinitely. 

Estimating precision 

The precision measurement is calculated using the Relative 

Percent Difference (RPD) between duplicate sample results per 

analyte. Precision estimates should be performed as soon as 

possible after receipt of laboratory results. 

Electronic data entry 

Approximately 10% of electronic data entries should be spot 

checked for errors on a random basis. If errors are found, 

another 10% are spot checked. 

Data archiving 

Sampling data and associated records are archived in boxes 

and stored at the GLKN Ashland office. Boxes are labeled with 

the year, project, and station number. 

Data validation Data validation is the process that determines whether quality 

control objectives for data collection were met. 

Data validation reports 

Data validation reports provide a narrative that discusses any 

deviations from QA/QC procedures and the impacts of those 

deviations. 

Data verification Data verification demonstrates that a dataset will qualify as 

credible data. 

Data verification reports Data verification reports document the results of the data 

verification procedure. 

Data qualification codes Data must be fully qualified before uploading to NPSTORET 

4.7 Methods for Long-Term Trend Analysis 

Following collection of at least three years of data at a given park, analyses more detailed than 

the data summaries described above may be conducted. Approaches to such detailed analyses 

may include estimation of interannual change, graphic approaches (e.g., comparison of mean and 

variability in a parameter in the current year versus during past years), and occasionally 

qualitative analysis (Guthery et al. 2001), as well as modeling, correlational analyses, and 

various parametric and nonparametric analyses. 
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After the first three sampling years of monitoring data are collected in each large rivers park 

(MISS and SACN) and periodically thereafter, more intensive analyses of change will be 

performed. In addition to repeated-measures, time-series, regression, and nonparametric 

equivalents of various methods such as regression, monitoring data may also be evaluated 

through Monte Carlo simulation analyses, Bayesian analyses, and comparisons of period means. 

For the latter-most approach, one is often interested in comparing values before and after an 

important event (e.g., change in management policy, remarkable anthropogenic disturbance, 

natural catastrophe, drought), and considers years within each of the two periods as replicates. 

Trends in parameters that are analyzed with respect to biotic and abiotic covariates can be 

examined, although cause-effect relationships may be investigated more thoroughly by NPS 

partners and collaborators (e.g., USGS-WRD, university investigators). 

In addition to analyzing each variable separately, flow-adjusted indicators of water quality that 

are not correlated and that naturally could be considered a homogeneous group of parameters can 

be analyzed collectively through multivariate ordinations (e.g., nonmetric multi-dimensional 

scaling; NMDS) of resource conditions through time, following West and Yorks (2002). This 

approach effectively integrates information across many indicators, and can suggest whether 

individual stations are all moving in the same direction in multidimensional ordination space. 

Furthermore, joint plots can be overlaid on the ordination, and can suggest which variables 

correlate most strongly to the direction of changes. 

Ideally, analyses of variability in selected parameters should also occur within the first two to 

three years of the monitoring program, to ensure that the variability in historical data correctly 

informed our a priori power analyses for determining the minimum number of sites needed to 

detect specific levels of change with 80% power. 

See SOP #9 for additional details on data summaries and analyses. 

4.8 Reporting Schedule 

As mentioned above, routine data summaries will occur annually for sites that are sampled 

within that year, and annual summary reports will be produced, with the primary audience being 

the parks. 

Comprehensive analyses of trend will occur for most parameters after three or more years of 

sampling. For stations that are located where no previous monitoring has occurred, three 

sampling periods is the minimum needed to establish a time series to assess temporal trend. 

However, past monitoring efforts suggest that much longer data series will be needed to achieve 

a dataset sufficiently powerful to detect meaningful levels of change (e.g., 20%) through time, 

given typically observed variability in water quality of lotic ecosystems. The target audience of 

the comprehensive reports of analyses will be the parks, the Network, both regional and Servicewide Inventory and Monitoring personnel, and the broader scientific community. These drafts 

will be reviewed internally and possibly sent to outside sources for further review, depending on 

the degree of analytical complexity of the methods and on the gravity of the implications and 

recommendations. 
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4.9 Report Format 

Both annual summaries and reports that include detailed analyses on trends should follow the 

format of a typical peer-reviewed journal article. The following outline is a good example of the 

type of report to be produced. 

TITLE PAGE 

(Title, Author(s), Participating Institutions, For Whom Prepared, and Date) 

TABLE OF CONTENTS PAGE 

EXECUTIVE SUMMARY PAGE (abstract) 

1.0 INTRODUCTION 

1.1 Background 

1.2 Justification for Study 

1.3 Objectives 

2.0 METHODS 

2. 1 Study area(s) 

2.2 Field method(s) 

2.3 Analytical method(s) 

3.0 RESULTS 

4.0 DISCUSSION 

5.0 MANAGEMENT IMPLICATIONS 

6.0 ACKNOWLEDGEMENTS 

7.0 LITERATURE CITED (if any) 

8.0 TABLES 

9.0 FIGURES 

10.0 APPENDICES (if any) 

Tables are appropriate for displaying simple data summaries, for example, mean annual values of 

water quality variables collected at one park. Figures are useful for comparisons or when 

examining relationships between variables, for example, concentration trends across years. 

Examples of some graphical formats are provided in Figures 12 and 13, with additional 

information on report format and presentation of data in SOPs #9 and #10. 
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Figure 12. Example of a box-and-whisker plot showing the median, interquartile range, 

first and third quartiles, and maximum and minimum values of average specific 

conductance values at a single monitoring station, 1990-2006. 

Figure 13. Examples of seasonal Kendall trend plots for three water quality variables. 

. 

1990 1994 1998 2002 2006

Year

200

250

300

350

A

VESPC

OND

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57 

5.0 Personnel Requirements and Training 

5.1 Roles and Responsibilities 

The final staffing for the inland lakes monitoring project will depend, in part, on the 

development and approval of a formal staffing plan for the Network. We envision a water quality 

monitoring program for lakes and rivers conducted by two or more field crews overseen by a 

project manager (GLKN aquatic ecologist, GS/11) and assistant to the project manager (GLKN 

aquatic ecologist GS/9). The field crews will consist of a crew leader at the GS/7 level, and a 

crew member at the GS/4 or GS/5 level. The assistant project manager serves as the crew leader 

for monitoring of large rivers. Each crew of two will be stationed at one of the parks and will 

travel to other parks as needed to implement monitoring. The Network will explore the 

possibility of sharing seasonal positions with the parks. When a park has an aquatic person on 

staff, the Network will make use of such existing staff expertise on the crew when possible, 

paying for the time spent on I&M monitoring activities, and will provide the same training to the 

park person as to the rest of the crew members. The field crews will monitor water quality in 

both rivers and lakes; the responsibilities, training, and qualifications of the crew are the same 

for both protocols. 

5.1.1 Project Manager 

The role of the project manager is to oversee all aquatic-related Network projects. Relative to 

monitoring water quality in large rivers, the individual is to serve as a liaison among other 

related water quality monitoring projects conducted by partners (e.g., state monitoring programs, 

Metropolitan Council of Environmental Services), park staff, other Network staff (field 

personnel, data manager), a contracted analytical laboratory, and other GLKN monitoring project 

managers. The individual will coordinate with resource management staff at the parks to ensure 

parks are informed of monitoring activities. Specific responsibilities of the project manager 

include the following:

• Coordinate field schedules and availability of supplies with field personnel 

• Develop a training program for field personnel 

• Develop, document, and oversee the implementation of standard procedures for field data 

collection and data handling 

• Coordinate logistics with park staff 

• Develop QA/QC measures for the project, supervise staff training, and conduct quality 

assurance checks of field sampling techniques at least once, mid-season, with each field 

crew 

• Contract with an analytical laboratory for analysis of water samples, ensure lab results 

meet program needs (e.g., QA/QC procedures, meaningful minimum detection limits for 

dilute waters, adequate reproducibility of replicate samples) 

• Supervise or perform data entry, verification, and validation 

• Summarize and analyze data, prepare reports 

• Serve as the main point of contact concerning data content 

• Manage the budget 
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The project manager will also work closely with the data manager in the following 

capacities: 

• Complete project documentation in NPSTORET (describing who, what, where, when, 

why, and how of a project) 

• Develop data verification and validation measures for quality assurance 

• Ensure staff members are trained in the use of database software and quality assurance 

procedures 

• Coordinate changes to the field data forms and the user interface for the project database 

• Identify sensitive information that requires special consideration prior to distribution 

• Manage the archival process to ensure regular archival of project documentation, original 

field data, databases, reports and summaries, and other products from the project 

• Define how project data will be transformed from raw data into meaningful information 

and create data summary procedures to automate and standardize this process 

• Establish meaningful liaisons with Minnesota and Wisconsin counterparts to promote 

sharing of data on a timely basis 

5.1.2 Assistant Project Manager 

This person will work with the project manager in all aspects of implementing the protocol for 

monitoring water quality in large rivers, but will also have duties related to inland lakes. The 

individual will take the lead in implementing this protocol for monitoring water quality of large 

rivers and will be stationed at SACN. Specific responsibilities include: 

• Represent the Network on the interagency Basin Team 

• Coordinate field schedules 

• Assist with coordination of supplies 

• Assist with training field personnel 

• Coordinate logistics with park staff 

• Perform field crew leader duties (outlined below in 5.1.3) or ensure duties are carried out 

• Help ensure all aspects of QA/QC are met 

• Perform data entry, verification, and validation 

• Train other staff in the use of database software 

• Assist with data analysis and report writing; take the lead in annual summary reports of 

large rivers monitoring

5.1.3 Field Personnel (Field Crew Member/Leader) 

The role of field personnel is to conduct all field work related to the monitoring project. Field 

personnel will include both a crew leader and a crew member. The crew leader is responsible for 

contacting the parks prior to each sampling event to ensure logistical requirements will be met. 

Responsibilities for both crew member and crew leader include the following: 

• Complete all training for field sampling, sample handling, and boat operation, if required 

by park 

• Complete all phases of field season preparation 

• Collect data and samples according to SOPs 
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• Complete analytical service request (ASR) and/or chain of custody (COC) forms; pack 

and ship samples to analytical lab 

• Maintain accurate field and office notes 

• Ensure that all QA/QC procedures are implemented 

• Maintain and calibrate equipment according to SOPs and manufacturers’ directions 

• Communicate progress and accomplishments with the project manager or assistant 

project manager during (if necessary) and after sampling at each park unit, and report any 

deviations from sampling protocols as necessary 

• Download, enter, and verify data into databases as required 

• Maintain documentation of important details of each field data collection period, 

including explanations of all deviations from standard procedures 

• Maintain hard copies of data forms and send original data forms to project manager on a 

regular basis 

• Represent the Network in a professional manner, assist in maintaining positive 

communication among the Network, park staff, and the public 

5.1.4 Data Manager 

The data management aspect of the monitoring effort is the shared responsibility of the data 

collectors first, then the project manager, and finally the Network data manager. Typically, field 

personnel are responsible for data collection, data entry, data verification, and validation. The 

data manager is responsible for data archiving, data security, dissemination, and database design. 

The data manager, in collaboration with the project manager, also develops data entry forms and 

other database features (as part of quality assurance) and automates report generation. 

5.2 Crew Qualifications 

The crew leader must have a bachelor’s or advanced degree in biology, chemistry, or other 

related physical or biological science. Field experience is mandatory and laboratory experience is 

preferred. Prior leadership experience and good decision-making skills are highly desirable, as is 

experience with boats, motors, and canoes. 

Crew members should have a background in biology, chemistry, or other related physical or 

biological science, although an undergraduate degree is not required. Prior field experience, 

including that with boats, motors, and canoes, is highly desirable and laboratory experience is 

preferred. 

All crew members must be physically fit, able to work long hours in inclement weather, and able 

to lift and carry heavy loads. 

5.3 Training Procedures 

Prior to data collection, field personnel must become familiar with the use, calibration, and 

maintenance of all meters and probes planned for use in the monitoring project. A combination 

of classroom and field training will be required prior to each field season. Personnel who were 

previously trained for this monitoring project will participate in a review of all methods and 

techniques. Specific details of the training procedures are covered in SOP #2 and will include: 

• Basic limnological concepts and field sampling techniques 
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• Review of all SOPs for project 

• Calibration, operation, and maintenance of all field and laboratory meters and probes 

used in the project 

• Methods for sample collection 

• Methods for cleaning equipment 

• Methods for handling and preserving samples 

• Completion of field data forms, sample labels, chain of custody forms, analytical service 

request forms 

• Data entry into NPSTORET 

• Completion of field and calibration logbooks 

• Use of GPS equipment 

• Park-specific training requirements (e.g., boat operation, navigation, radios) 

• NPS-specific training (e.g., computer use, credit card, travel) 
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6.0 Operational Requirements 

6.1 Annual Workload and Field Schedule 

The annual workload and schedule for the monitoring of water quality in large rivers must be 

viewed within the context of the other planned aquatic monitoring activities to be conducted by 

GLKN aquatic staff. We prepared the estimated workload and schedule for monitoring of large 

rivers inland lakes together, but anticipate additional aquatic protocols in the future (e.g., 

wadeable streams). As these additional protocols become part of the GLKN monitoring program, 

the workloads are likely to change. 

We will monitor water quality at the two large river park units once a month during the open 

water season (approximately March to November). The time it takes to conduct field work is 

always weather dependent, however we estimate sampling to take two days at MISS and six days 

at SACN. Estimates of time required to sample at each park (explained in more detail, below, 

under staff salaries) assume minimal weather-related delays. Overtime and compensatory times 

are not factored in.

6.2 Facility and Equipment Needs 

The field crew needs a facility with a sink and counter-top space where they can calibrate 

instruments, clean and store equipment, and process samples. They also need a refrigerator and 

freezer for storing samples prior to shipment to an analytical laboratory, and secure space for 

storing a boat, motor and gasoline, canoe, and other field equipment. Currently, MISS has none 

of these facilities; SACN has adequate space that is shared by GLKN and park natural resources 

staff. 

6.3 Startup Costs and Budget Considerations 

6.3.1 Equipment and Initial Start-up Costs 

Each sampling crew requires its own equipment because water quality sampling will occur at 

seven or more parks each year (including inland lakes and large rivers), widely separated in 

distance. Some of the parks already have some of the necessary sampling gear and equipment, 

and the Network has acquired gear as funds permitted. When possible, we will coordinate with 

the parks in the use of their equipment. Because neither MISS nor SACN has an ongoing water 

quality monitoring program, all equipment required for basic water quality monitoring at these 

two parks will have to be purchased by the Network.

Start-up costs are expected to be approximately $50,300 (Table 24); annual estimated costs of 

equipment and supplies are approximately $9,900. Both initial and annual costs include 

equipment and supplies that will be used to monitor water quality of both inland lakes and large 

rivers. Monitoring of large rivers alone will cost approximately one third of these costs, or 

$16,767 in start-up costs and $3,300 for annual equipment and supplies. 
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Table 24. Expected start-up costs of water quality monitoring program in large rivers and inland 

lakes of the Great Lakes Network, including one-time purchases and routine expenses. * 

indicates one-time start-up expenses; other expenses are expected to reoccur periodically or 

annually. 

6.3.2 Staff Salaries 

Project Manager: The project manager’s salary will be split between I&M and WRD funding 

(Table 25). 

Assistant Project Manager: In 2007, the Network hired a permanent GS/9 subject-to-furlough 

ecologist to assist the project manager. This person is responsible for taking the lead in sampling 

for large rivers, but will also have responsibilities related to the inland lakes protocol. Salary for 

this position will be shared between I&M and WRD funding. 

Item Quantity Cost Each Total Cost

multi-probe sonde* 3 7000 21,000

GPS unit and software* 3 500 1500

flow meter* 1 2500 2500

secchi disk and non-stretch line* 3 130 390

digital camera* 3 400 1200

canoe and accessories* 2 1200 2400

boat, trailer* 1 8000 8000

benchmarks* 60 10 600

anchor* 3 50 150

integrated tube sampler* 10 20 200

Van Dorn* 4 300 1200

electric pump for filtering* 3 350 1050

benchtop pH meter* 3 400 1200

transparency tube* 3 55 165

refrigerator/freezer* 1 500 500

laptop computer* 3 2500 7500

hand pump 5 125 625

certified thermometer* 4 30 120

Subtotal $50,300

miscellaneous field equipment (boots, buckets, PFDs,) 2000 2000

replacement probes 400 400

miscellaneous lab equipment (glassware, forceps, basins) 1500 1500

other consumables (calibration standards, acid, filters) 2500 2500

shipping samples to analytical labs 3500 3500

Subtotal $9,900

TOTAL $59,900
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Field Crew Member: We will need a field crew member for approximately 12 pay periods, and 

will use existing staff during the early and late sampling months if necessary. When possible, we 

will share the costs and time of a seasonal biological technician with one of the parks. 

Data Manager: The data manager’s salary will be covered by the I&M program. 

Table 25. Estimated annual costs of staff salaries and benefits for monitoring water quality at the 

large river parks of the Great Lakes Network, excluding data manager. 

Position Amount of Time Cost 

Project manager 50% WRD $39,076 

Assistant project manager 50% WRD $30,189 

Crew member 1039 hours $13,070 

Total $82,335 

6.3.3 Vehicle and Travel 

Estimated vehicle and travel costs for sampling at MISS and SACN are based on the following 

assumptions: 

• The Network will use a GSA vehicle 

• Because MISS has extremely limited parking space, the fleet vehicle and boat will be 

kept at SACN 

• Samples will be processed at SACN at the end of each sampling day 

• Lodging and per diem costs are minimal, but may include one night in travel status for 

two people each round of sampling at SACN; we expect no lodging or per diem costs 

associated with sampling at MISS 

Under these assumptions, annual vehicle and travel costs associated with sampling at MISS total 

approximately $3,700 and at SACN, $5,500 (Table 26). Costs are likely to increase, perhaps 

drastically, in the future. 

Table 26. Estimated travel costs associated with monitoring water quality at the two large river 

parks of the Great Lakes Network. 

Costs Category MISS SACN 

GSA vehicle, $265/month (pick-up truck) 3180 3180

Mileage for GSA vehicle @ 0.22/mile 495 1980

Lodging (9 rounds of sampling) 0 140

Per diem (9 rounds of sampling) 0 234

Total annual costs $3,675 $5,534
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6.3.4 Analytical Laboratory Costs 

Monitoring guidelines established by the Water Resources Division (WRD) include strong 

recommendations for selecting an analytical laboratory that has been accredited by the federal 

National Environmental Laboratory Accreditation Program (NELAP) (Irwin 2004, 2006). The 

Network assesses the differences in detection and reporting limits among NELAP-approved, 

state accredited, and research laboratories prior to selecting a contract lab. The laboratory 

selected by GLKN must be able to detect and report levels appropriately low, such that changes 

in water quality variables can be detected early in the naturally low strength waters occurring 

throughout the Network. The laboratory selected must meet the detection limits detailed in SOP 

#12 and have a rigorous QA/QC plan. For the purpose of estimating a budget for monitoring 

water quality in large rivers, we use the costs quoted by White Water Associates, a GSAcontracted and NELAP-certified laboratory, in Table 27. The quotes from the other laboratories 

are included as examples of what our costs might be if we selected one of them, instead. 

We expect to measure nutrients (TP, TN, NO3+NO2-N, NH4-N), total suspended solids, and 

chlorophyll-a each sampling visit, or nine times per survey-year, and the remaining parameters 

three times per survey-year. Annual estimated laboratory analysis costs are approximately 

$6,800 at MISS and $15,000 at SACN, excluding the costs of blanks and replicates (Table 28). 

6.3.5 Total Estimated Annual Costs 

Estimates for starting a long-term water quality monitoring program ($16,767) and the annual 

implementation costs (Table 29), at the two large river parks are high and consume a substantial 

portion of the WRD-funded portion of the GLKN I&M budget. The Network will pursue 

opportunities for cost-sharing with parks, both for equipment and personnel. 

Table 27. Estimates of laboratory costs (2007 prices) for analysis of standard water quality 

parameters. ‘NA’ = not available. 

 Parameter 

White Water Assoc., 

GSA contract, 

NELAP certified lab 

Natural 

Resources 

Research Institute

Wisconsin State Lab of 

Hygiene, NELAP 

certified lab 

Alkalinity $10.30 $9.20 $23.75 

DOC $20.60 $18 $55.35 

Cl See SO4 See SO4 $18.75 

SO4 $25 (Cl w/ SO4) $23 (Cl w/ SO4) $12.50 

Na, K, Mg, Ca $33 $23 $20 

TP $12 See TN $14.50 

TN $28 (as TKN) $30 (TP & TN) $15 

NH4-N $12 $12 .32 $12.68 

NO3+NO2-N $12 $13.44 $12.68 

chlorophyll-a $40 $34.68 

SiO2 $20.60 11.40 $21.25 

TSS $10.30 $16 $22 

set-up fee 0 0 $10 
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Table 28. Annual estimated costs for laboratory analyses at the two large river parks of the Great 

Lakes Network. 

Table 29. Estimated total annual costs for monitoring water quality at the two large river parks of 

the Great Lakes Network. 

Park Salary Travel Lab Equipment and 

Consumables* Total 

MISS 1⁄2 of $82,335 = $41,168 $3,675 $6,790 $1,650 $53,283 

SACN 1⁄2 of $82,335 = $41,168 $5,534 $14,938 $1,650 $63,290 

* calculated as 1/8 of total annual expenses, split 8 ways among GLKN parks with large 

 rivers and inland lakes 

6.4 Procedures for Revising and Archiving Previous Versions of the Protocol 

As our water quality monitoring program matures, revisions to both the protocol narrative and 

specific standard operating procedures (SOPs) are likely. Documenting changes and archiving 

copies of previous versions of the protocol and SOPs are essential for maintaining consistency in 

the collection of data and for appropriate interpretation of data summaries and analyses. The 

NPSTORET database contains a field for each monitoring component that identifies which 

version of the protocol was used when the data were collected. 

The rationale for dividing a sampling protocol into a protocol narrative with supporting SOPs is 

based on the following: 

• The protocol narrative is a general overview of the protocol that gives the history and 

justification for doing the work and an overview of the sampling methods, but does not 

provide all methodological details. The protocol narrative will only be revised if major 

changes are made to the protocol. 

• The SOPs are specific step-by-step instructions for performing a given task. They are 

expected to be revised more frequently than the protocol narrative. 

• Usually, when a SOP is revised, it is not necessary to revise the protocol narrative to 

reflect the specific changes made to the SOP. 

All versions of the protocol narrative and SOPs will be archived. 

Costs Laboratory Parameters MISS SACN 

Analytes measured 9x/yr 

(nutrients, Tchl-a, TSS; $1029/site) $5,145 $11,319 

Analytes measured 3x/yr 

(ions, alkalinity, DOC, SiO2; $328/site) $1,640 $3,608 

Total ($1,358/site) $6,790 $14,938 
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The steps for changing the protocol (either the protocol narrative or the SOPs) are outlined in 

Revising the Protocol (SOP #13). Each SOP contains a Revision History Log that must be 

updated each time a SOP is revised, to explain why the change was made and to assign a new 

version number to the revised SOP. The new version of the SOP or protocol narrative should 

then be archived in the appropriate folder of the GLKN database structure. 
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7.0 Literature Cited 

Ayers, M., R. Brown, and G. Oberts. 1985. Runoff and chemical loading in small watersheds in 

the Twin Cities Metropolitan Area, Minnesota. U.S. Geological Survey Water-Resources 

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Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

73 

Standard Operating Procedures 

SOP #1: Pre-Season Procedures 

SOP #2: Training and Safety 

SOP #3: Using a GPS 

SOP #4: Site Establishment 

SOP #5: Decontamination of Equipment to Remove Exotic Species 

SOP #6: Field Measurements and Water Sample Collection 

SOP #7: Processing Water Samples and Analytical Laboratory Requirements 

SOP #8: Data Entry and Management 

SOP #9: Data Analysis 

SOP #10: Reporting 

SOP #11: Post-Season Procedures 

SOP #12: Quality Assurance/Quality Control 

SOP #13: Revising the Protocol 

Standard Operating Procedure #1: 

Pre-Season Preparation 

Version 1.0 

In Large Rivers Water Quality Monitoring Protocol 

Prepared by 

Suzanne Magdalene and Daniel Engstrom 

St. Croix Watershed Research Station 

16910 152nd. St. North 

Marine on St. Croix, Minnesota 55047 

and 

Joan Elias (contact author) 

National Park Service 

Great Lakes Inventory and Monitoring Network 

2800 Lake Shore Drive East 

Ashland, Wisconsin 54806 

joan_elias@nps.gov 

August 2008 

Suggested citation: Magdalene S., D.R. Engstrom, and Elias J. 2008. Standard operating 

procedure #1: Pre-season preparation. in Magdalene S., D.R. Engstrom, and J. Elias. 2008. Large 

rivers water quality monitoring protocol, Version 1.0. National Park Service, Great Lakes 

Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/060. National Park Service, Fort 

Collins, Colorado.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #1, page ii

Contents 

 Page

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

1.0 Introduction..........................................................................................................................1 

1.1 Read the Entire Protocol ......................................................................................................2 

1.2 Prepare Calendar of Planned Field Sampling ......................................................................2 

1.3 Review Checklists of Equipment and Supplies ...................................................................3 

1.4 Confirm/Apply/Renew Research and Collecting Permits ...................................................3 

1.5 Review Documentation for Sample Collection and Processing ..........................................3 

1.6 Update Field and Office Binders .........................................................................................3 

1.7 Clean and Test Equipment...................................................................................................5 

1.8 Vehicle, Boat, and Safety Gear............................................................................................5

1.9 Training and Safety..............................................................................................................5 

1.10 Field Reconnaissance...........................................................................................................5 

1.11 Travel Arrangements ...........................................................................................................6 

1.12 Communicate with Supervisor.............................................................................................6 

1.13 Equipment Blanks................................................................................................................6 

1.14 Literature Cited ....................................................................................................................6 

Tables 

 Page 

Table 1. Checklist of activities to be conducted prior to sampling large rivers...............................1 

Table 2. Example of calendar of planned field sampling ................................................................2 

Table 3. Checklists of the large rivers water quality monitoring protocol ......................................3 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #1, page iii

Revision History Log 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project manager must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the header of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log: 

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #1, page iv

Acknowledgements 

We wish to thank Rich Axler and Elaine Ruzycki for contributing to earlier drafts of this 

standard operating procedure. We also appreciate the work of others (O’Ney 2005, USGS 2005), 

whose documents we relied upon for guidance.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #1, page 1

1.0 Introduction 

Prior to the field season, many preparations must be completed to ensure sampling can be 

undertaken according to schedule. The field season for sampling large rivers of the Great Lakes 

Network parks is generally from March through November. All details for the season need to be 

planned well in advance. Field preparations should begin in January to allow enough time for 

ordering new supplies and equipment, if necessary. Table 1 provides a checklist and general 

guidance for activities conducted prior to sampling. Many of these activities are discussed in 

more detail in other SOPs. 

Table 1. Checklist of activities to be conducted prior to sampling large rivers. 

√ Activity Description 

 Prepare calendar of planned field trips Includes sampling dates, locations, personnel 

 Review sampling methods to determine if 

revision is needed 

Check web reference to see if method has been updated 

from version currently used 

 Review checklists of equipment and 

supplies required; prepare list of items to 

be ordered 

Check each standard operating procedure for detailed 

equipment lists; check expiration dates of reagents, 

standards, and other chemicals 

 

Order supplies 

Includes calibration standards for multiparameter 

instruments, pre-sterilized and/or pre-cleaned bottles for 

sample collection (if not provided by the contract 

analytical laboratory), sample preservation solutions 

 

Clean and test equipment; charge or 

replace batteries as needed 

Includes multiprobe, integrated sampling tube, Van Dorn, 

back-up instruments, ropes, batteries, 

thermistors/thermometers, camera, GPS unit, cell phone or 

radio 

 Prepare equipment blanks Must be done annually 

 Obtain permission for site access, if 

necessary 

 Confirm current research and collection 

permits for in-park sites 

 Check field vehicle and boat for safety 

equipment and supplies 

Includes material safety data sheets, flares, flashlight, 

gloves, extra sampling bottles, etc. 

 Update field binder Include maps, site information, field forms, sampling 

procedures 

 Prepare headers on field data forms, chain 

of custody forms, analytical service request 

forms, bottle labels 

Header information should be cross-checked with 

metadata to permit entry into NPSTORET 

 

Review sample collection, processing, and 

documentation information 

Includes methods, lab codes, bottle type, and sample 

collection and processing procedures; sample shipment; 

quality control samples. (Refer to SOPs #6 and #7) 

 Make travel reservations and arrangements 

as needed 

 Provide supervisor with field trip and callin (check-in) schedule 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #1, page 2

1.1 Read the Entire Protocol 

Periodically read through the entire protocol, including all standard operating procedures (SOPs). 

Be sure to understand the purpose for which the various types of data will be collected and 

review the SOPs for the types of measurements and samples needed. Be alert for portions of the 

protocol or SOPs that may be in need of revision, and bring these sections to the attention of the 

appropriate supervisor. 

1.2 Prepare Calendar of Planned Field Sampling 

Well in advance of the field season, prepare a calendar of sampling dates for the entire season. 

Allow for the possibility of bad weather days, when sampling may have to be postponed. Include 

the location of sampling, dates, parameters to be measured, personnel, and any additional 

relevant notes (Table 2). 

Table 2. Example of calendar of planned field sampling. 

Location Sampling 

Dates WQ Variables Personnel Notes 

MISS River March 1-4 core suite, chl-a, TP, TN, alk, 

NO2+NO3-N, NH4-N, TSS, alk, 

cations, anions, DOC, SiO2, 

VanderMeulen, 

park biotech 

Quarterly sampling of 

ions, etc. 

MISS River April 1-4 core suite, chl-a, TP, TN, alk, 

NO2+NO3-N, NH4-N, TSS 

VanderMeulen, 

park biotech 

Check rating curve 

calibration 

MISS River May 1-4 core suite, chl-a, TP, TN, alk, 

NO2+NO3-N, NH4-N, TSS 

VanderMeulen, 

park biotech 

INDU Lakes May 15-20 core suite, chl-a, TP, TN, alk, 

NO2+NO3-N, NH4-N, cations, 

anions, DOC 

VanderMeulen, 

park biotech 

MISS River June 1-4 core suite, chl-a, TP, TN, alk, 

NO2+NO3-N, NH4-N, TSS, 

cations, anions, DOC, SiO2, 

VanderMeulen, 

park biotech 

Quarterly sampling of 

ions, etc. 

MISS River July 1-4 core suite, chl-a, TP, TN, alk, 

NO2+NO3-N, NH4-N, TSS 

VanderMeulen, 

park biotech 

INDU Lakes July 15-20 core suite, chl-a, TP, TN, alk, 

NO2+NO3-N, NH4-N 

VanderMeulen, 

park biotech 

If stratified, collect 

bottom water sample 

MISS River August 1-4 core suite, chl-a, TP, TN, alk, 

NO2+NO3-N, NH4-N, TSS 

VanderMeulen, 

park biotech 

Check rating curve 

calibration 

MISS River Sept 1-4 core suite, chl-a, TP, TN, alk, 

NO2+NO3-N, NH4-N, TSS, 

cations, anions, DOC, SiO2 

VanderMeulen, 

park biotech 

Quarterly sampling of 

ion, etc. 

MISS River October 1-4 core suite, chl-a, TP, TN, alk, 

NO2+NO3-N, NH4-N, TSS 

VanderMeulen, 

park biotech 

INDU Lakes Oct. 15-20 core suite, chl-a, TP, TN, alk, 

NO2+NO3-N, NH4-N, cations, 

anions, DOC 

VanderMeulen, 

park biotech 

MISS River November 1-4 core suite, Tchl-a, TP, TN, alk, 

NO2+NO3-N, NH4-N, TSS 

VanderMeulen, 

park biotech 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #1, page 3

1.3 Review Checklists of Equipment and Supplies 

Checklists help ensure that equipment and supplies will be ordered on time, data collection 

activities will be completed appropriately, and data quality objectives will be met. Review the 

detailed equipment lists that are included with each standard operating procedure (Table 3). Pay 

attention to expiration dates on reagents, calibration standards, and all other chemicals. Prepare a 

list of equipment and supplies that must be ordered and present it to the project manager. 

Table 3. Checklists of equipment and supplies for monitoring water quality of large rivers. 

Checklist Location 

Safety equipment checklist SOP #2 

Decontamination equipment and supplies SOP #5 

Field supplies and equipment checklist SOP #6 

Laboratory equipment and supplies SOP #7 

1.4 Confirm/Apply/Renew Research and Collecting Permits 

For sampling stations located within park boundaries, a Research and Collecting Permit must be 

obtained before any work can be done. To renew or apply for the permit, go to the following 

website: http://science.nature.nps.gov/research/ac/apps/appInstructions

Follow the directions for renewing an existing permit, or if your project is not already in the 

system, then follow the directions to apply for a new permit. Work with the research coordinator 

at each park. 

1.5 Review Documentation for Sample Collection and 

Processing 

Conduct a thorough review of “Field Measurements and Water Sample Collection” (SOP #6) 

and “Processing Water Samples and Analytical Laboratory Requirements” (SOP #7). 

Check with the project leader to determine current contract analytical laboratory information. 

Contact the laboratory to verify lab codes and procedures. Obtain copies of Analytical Services 

Request (ASR) and Chain of Custody (COC) Forms. 

1.6 Update Field and Office Binders 

Field binders should contain reference information specific to each sampling station, including 

maps, photos, previous data, field forms, and summaries of sampling and QA/QC procedures. 

The field binder should be taken along on each sampling trip. The office binder should contain 

reference information relevant to general field sampling procedures with tabs identifying each 

procedure for easy access during field work, including QA/QC reminders, a copy of the protocol 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #1, page 4

narrative and all SOPs, copies of equipment instructions and troubleshooting; extra field forms, 

material safety data sheets for field supplies that contain hazardous chemicals or materials, and 

analytical service request and chain of custody forms. 

Each year, prior to the sampling season, the field binder for each monitoring site should be 

reviewed and the following information updated as needed: 

 

• Location of river level gage (if one is present). 

• Location of sample-collection sites. Review field notes for any indication that the 

location for sample collection may need revision. Update protocol if necessary. 

• Name of landowner, tenant, or other responsible party. If the sampling station is located 

on private land, ownership may change. Verify. 

• Current copy of research and collection permit (if site is located within NPS boundaries). 

Check dates on permit. Renew/apply as described above. 

• Site access instructions (e.g., call owner or site operator before arrival at site, obtain key 

to unlock security gate). Confirm contact person, procedure, and phone numbers. 

• Photographs to document site conditions. Take new digital photograph annually and 

when conditions have changed. 

• Maps to site (state and local). Review map for accuracy; update if necessary. 

• Review previously collected chemical, physical, and biological data. A summary of 

previously-collected data or copies of previous field data sheets should be in the field 

folder so that water column profiles and water clarity data can be compared to previous 

surveys. Familiarity with previously collected data is a critical quality assurance (QA) 

element for early detection of possible instrument malfunction.

• Data collection field forms and sample bottle labels. Prepare as much of the field forms 

as possible in advance. For each station, complete the header information, including the 

project ID, station ID and station name and other required metadata for NPSTORET. 

Place enough field forms in field folder to last entire field season. 

Each year, prior to the sampling season, the office binder should be reviewed and the following 

information updated as needed: 

 

• Safety information (SOP #2). Verify/update “Medical Information Form for Field 

Personnel” and “Emergency Contact Form”. 

• Decontamination procedures (SOP #5). Ensure that the most recent information on 

presence of exotic species and need for decontamination of equipment has been 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #1, page 5

incorporated into the Hazard Analysis and Critical Control Plan (HACCP) for each park. 

Update office binder with the latest information. If the order of sites to be sampled must 

change due to new infestations, be sure sampling schedule is updated. 

• Sampling schedule and instructions. Ensure the following information from SOP #6 

(Field Measurements and Water Sample Collection) is included in the office binder: 

laboratory analyses to be requested and associated codes, when to collect samples, bottle 

types needed for each analytical schedule, preservation requirements, quality control 

sample requirements, and shipping instructions. Verify information is correct and report 

and reconcile any discrepancies to supervisor. 

• Ensure that copies of the current field procedures are included in the office binder. 

Include calibration and maintenance procedures specific to the instruments to be used. 

• Analytical service request forms, data collection field forms, chain of custody forms, 

sample bottle labels. Prepare as much of the field forms as possible in advance. For each 

station, complete the header information, including the project ID, station ID and station 

name and other required metadata for NPSTORET. Place enough blank field forms in 

office folder to last entire field season.

 

1.7 Clean and Test Equipment 

Clean and test all sampling equipment, including multiparameter sonde, Van Dorn and integrated 

tube samplers, camera, GPS units, and any back-up meters. Check calibration of metered ropes 

to ensure accurate depth measures. Start each new field season with fresh batteries and replace 

spares in field tool kit. 

1.8 Vehicle, Boat, and Safety Gear 

Check maintenance schedule of field vehicle and arrange maintenance, if needed. Check boats 

and vehicle for safety equipment such as MSDSs, flares, spare tire, triangles, cones, first aid kit. 

Prepare a list of supplies needed and present list to supervisor. If using a trailer, ensure that taillights are in working order. Check that field tool-kit is complete and replace tools, as needed. 

1.9 Training and Safety 

Keep current with training and the laboratory requirements associated with your data collection 

activities. New technicians will need basic skills training, including classroom instruction, handson training, and pilot-testing of equipment. Continuing field staff should attend annual refresher 

training. If boat training is needed, be sure to schedule the training with the park early in the 

season. Initial and periodic refresher courses in basic first aid and CPR are required. 

1.10 Field Reconnaissance 

Make field reconnaissance trips, if possible. Visit the sampling sites to be sure that conditions 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #1, page 6

have not changed from the previous year. Note conditions that could affect sampling operations, 

such as the seasonal high or low water levels, or peculiarities of site access. In parks where rivers 

are accessible via roads, ensure all roads are passable and landing areas are accessible. In cases 

where rivers are not accessible via roads, communicate with park backcountry staff to learn of 

potential trail closings or other hindrances to sampling. 

1.11 Travel Arrangements 

Make travel arrangements. Because hotel and campground reservations may be difficult to 

impossible to obtain at certain times of year, it is important to review the sampling schedule and 

plan ahead. Submit park housing requests well in advance of the sampling season. 

1.12 Communicate with Supervisor 

Ensure the project manager is informed of supply needs, problems with instruments, changes in 

sampling schedule, changes in sampling site conditions, and other needs that may have an impact 

on the project budget, data collection, schedule, or sampling design. 

1.13 Equipment Blanks

An equipment blank should be conducted annually, at least four weeks prior to using the 

equipment in the field to ensure adequate time for analysis and review of results. Equipment 

blanks should be collected in a designated clean area of the sample processing laboratory. The 

blank consists of deionized water that is passed sequentially through each component of the 

sample collection and processing equipment. Equipment blanks should also be conducted when a 

new cleaning procedure is instituted and when new equipment will be used for the first time. 

Procedure 

• Fill the cleaned integrated sampling tube or Van Dorn with deionized water (DIW). 

• Dispense water from integrating tube or Van Dorn into cubitainer or carboy. 

• From cubitainer or carboy, dispense water directly into appropriate analyte bottles, or 

filter first, according to instructions for each analyte (SOP #7). 

• Preserve samples according to instructions for each analyte in SOP #7. 

If the equipment-blank data indicate that the equipment does not introduce contaminants that will 

bias study results, sampling can proceed. If the equipment-blank data indicate unacceptable 

concentrations of analytes of interest, the cause must be identified and the equipment or cleaning 

procedures must be changed or modified before sampling can proceed. 

1.14 Literature Cited

O’Ney, S.E. 2005. Standard operating procedure #2: Pre-season activities, Version 1.0. in

Regulatory water quality monitoring protocol, Version 1.0, Appendix E. Bozeman (MT): 

National Park Service, Greater Yellowstone Network. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #1, page 7

USGS. 2005. National field manual for the collection of water-quality data: U.S. Geological 

Survey Techniques for Water-Resources Investigations, book 9, chaps. A1-A9.

Standard Operating Procedure #2: 

Training and Safety 

Version 1.0 

In Large Rivers Water Quality Monitoring Protocol 

Prepared by 

Joan Elias 

National Park Service 

Great Lakes Inventory and Monitoring Network 

2800 Lake Shore Drive East 

Ashland, Wisconsin 54806 

joan_elias@nps.gov 

August 2008 

Suggested citation: Elias, J. 2008. Standard operating procedure #2: Training and safety. in

Magdalene S., D.R. Engstrom, and J. Elias. 2008. Large rivers water quality monitoring protocol, 

Version 1.0. National Park Service, Great Lakes Network, Ashland, Wisconsin. 

NPS/GLKN/NRR—2008/060. National Park Service, Fort Collins, Colorado.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #2, page ii

Contents 

 Page

Revision History Log.................................................................................................................... iii 

Acknowledgements....................................................................................................................... iv 

2.0 Introduction.........................................................................................................................1 

2.1 Pre-Season Classroom Training..........................................................................................1 

 2.1.1 Hydrological Concepts...............................................................................................1 

 2.1.2 Understanding the Protocol and Standard Operating Procedures..............................1 

 2.1.3 First Aid and Cardio-Pulmonary Resuscitation (CPR)..............................................1 

2.2 Hands-on Training ..............................................................................................................2 

 2.2.1 Use of a Multisensor Water Quality Instrument........................................................2 

 2.2.2 Use of a Global Positioning System (GPS) ...............................................................2 

 2.2.3 Field Methods ............................................................................................................2 

 2.2.4 Processing Water Samples.........................................................................................3 

 2.2.5 Cleaning Field and Laboratory Equipment................................................................3 

 2.2.6 Boat Training .............................................................................................................3 

2.3 Safety Procedures................................................................................................................3 

 2.3.1 USGS Field Manual...................................................................................................3 

 2.3.2 Basic Safety Preparation............................................................................................4 

 2.3.3 Medical Forms and Safety Equipment Checklists.....................................................5 

 Emergency Contact Form..........................................................................................6 

 Medical Information Form........................................................................................7 

 General Safety Equipment Checklist ........................................................................8 

 Personal Protective Equipment Checklists................................................................9 

 Checklists for Vehicles and Vehicular Laboratories...............................................10 

 Watercraft Checklists ..............................................................................................11 

2.4 Literature Cited .................................................................................................................12 

 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #2, page iii

Revision History Log 

 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project leader and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log: 

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #2, page iv

Acknowledgements 

The safety related portions of this standard operating procedure were adapted from the 

GreaterYellowstone Network’s SOP on safety (O’Ney 2005), with heavy reliance on the U.S. 

Geological Survey’s manual for collecting water quality data (Lane and Fay 1997). 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #2, page 1

2.0 Introduction

Prior to collecting data and water samples in the field, the field crew members must be trained in 

the techniques and procedures that will be used throughout the season. Familiarity with the 

protocol and standard operating procedures (SOPs), as well as with boats, equipment, and basic 

safety standards, are critical to the success of the water quality monitoring project. This SOP 

includes procedures for training in the specific water quality related skills and knowledge 

necessary for collecting good data and understanding those data. The crew must be also trained 

in specific safety procedures to ensure their safety and that of others. 

The project manager will conduct or arrange for all training needed prior to the field season. 

2.1 Pre-Season Classroom Training

It is desirable to begin training well before the field season begins to allow adequate time for 

thorough understanding of field and laboratory procedures and to obtain certification in boat use 

and first aid. Field crew leaders must undergo all of the following training. Training in boat use 

and first aid is required of other field crew members, and training in the remaining areas is 

desirable. 

2.1.1 Hydrological Concepts 

An understanding of basic hydrological concepts is useful for recognizing bad or illogical data in 

the field. For example, a dissolved oxygen reading of 30 mg/L may indicate a malfunction of the 

multiparameter sensor, or something as simple as fouling of the probe. Recognition of the 

problem at the time it occurs allows for immediate adjustment in the field, for example cleaning 

the membrane on the probe or changing the batteries, so that good data can still be collected. 

The field crew leaders, and if possible, other crew members, will study select modules of the 

Water on the Web (2004) curricula (http://waterontheweb.org/curricula). The modules will be 

selected by the project manager and will include those on lake surveys (e.g., field profiles, 

sample collection, laboratory methods). Individual study will be followed with group discussion 

and/or individual discussion with the project manager or a hydrologist. 

2.1.2 Understanding the Protocol and Standard Operating Procedures 

Reading and understanding the entire protocol and all SOPs are crucial prior to initiating field 

work. The project manager will allow adequate time for all field crew members to complete this 

step to ensure success of the project. Field and laboratory related SOPs will also be covered as 

part of the hands-on training, described below. 

2.1.3 First Aid and Cardio-Pulmonary Resuscitation (CPR) 

Training in the basic medic/first aid and Heartsaver AED, which includes CPR and use of an 

automated external defribrillator (AED), is required for all crew members and will be paid for by 

the Network. Certification is valid for two years. Training and certification should be acquired 

prior to the field season. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #2, page 2

2.2 Hands-On Training

In addition to the classroom training described above, a variety of hands-on training and practice 

prior to the first sampling period will help ensure high quality data collection. Familiarity with 

the use and maintenance of equipment, procedures for collecting and processing water samples, 

techniques for cleaning field and laboratory equipment, and safe use of watercraft are essential to 

the success of the water quality monitoring project. Field crew leaders are required to complete 

all of the following training; other field crew members should also complete the training, if 

possible, although it is not required. 

2.2.1 Use of a Multisensor Water Quality Instrument 

Each type of multisensor instrument comes with specific instructions on use and care. Guidelines 

for calibration and use of multisensor instruments are included in SOP #6, however it is 

important to use the instruction manual specific to each instrument. Check the manufacturers’ 

websites for updates or changes to instructions. 

Training in the use of a multisensor instrument will include the following: 

• Calibration procedures and acceptance criteria 

• Keeping a calibration log 

• Maintenance, including replacing fluids and membranes 

• Creating files on the data logger 

• Storing data on the data logger 

• Downloading data to a laptop computer 

• Use of the instrument in a field setting, including depth profiles and equilibration 

• Troubleshooting 

Crew members will have the opportunity to practice the skills learned prior to the actual 

sampling until they are comfortable with the use of the instrument. 

2.2.2 Use of a Global Positioning System (GPS) 

Location information must be gathered via GPS for each site during each visit. Training in the 

use of a GPS will include navigation to a known location, acquiring location information, storing 

data, and downloading data. Details on the use of a GPS can be found in SOP #3. 

2.2.3 Field Methods 

In addition to collecting data with the multisensor instrument, a field data sheet must be 

completed, a water sample must be collected, and the water level must be determined at each 

site. Prior to the field season, the field crew will receive training in and have the opportunity to 

practice the following: 

• completing the field data sheet 

• using an integrated sampling tube 

• using a Van Dorn sampler 

• reading a staff gage 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #2, page 3

• decontaminating equipment between river sections to avoid transfer of species from 

one area to another, and determining when decontamination is necessary 

• following QA/QC procedures 

2.2.4 Processing Water Samples 

Whether the water samples are processed for further analytical laboratory analysis in the field or 

back at the office or lab, strict procedures must be adhered to (see SOP #7). Crew members will 

be trained in, and will have the opportunity to practice the following techniques: 

• Handling water samples so as to avoid contamination 

• Rinsing and filling bottles from the analytical laboratory 

• Preserving samples for various chemical analyses 

• Filtering samples for various analyses 

• Packing samples for shipment to analytical laboratory 

• Filling out chain of custody forms 

• Following QA/QC procedures 

2.2.5 Cleaning Field and Laboratory Equipment 

Field and laboratory equipment must be cleaned between sites or samples to avoid contamination 

with water from the previous sampling site. Training in proper techniques will include: 

• Cleaning equipment with P-free detergent 

• Setting up an acid bath 

• Cleaning equipment with an acid bath 

• Rinsing with distilled or de-ionized water 

2.2.6 Boat Training 

Prior to operating a NPS boat or canoe, training and certification are required. The crew leader 

must receive the training and obtain certification, and it is highly desirable for the remaining 

crew members to do so as well. The project manager will arrange for training prior to the field 

season through one of the several GLKN parks that offer it. 

2.3 Safety Procedures 

Safety of field personnel should always be the first concern in conducting a sampling program 

and in the selection of sampling sites. Numerous safety issues and concerns are associated with 

implementing a water quality monitoring project that includes extensive field work and 

sampling. Field personnel routinely come into direct and indirect contact with waterborne 

pathogens, chemicals, and potentially hazardous plants and animals. Field work requires an 

awareness of potential hazards and knowledge of basic safety procedures. Advanced planning 

can reduce or eliminate many safety hazards. 

2.3.1 USGS Field Manual 

This SOP is meant to be used in conjunction with Chapter A9 of the USGS National Field 

Manual (Lane and Fay 1997), which contains more complete information about potential hazards 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #2, page 4

that water quality monitoring field personnel may encounter during field work and the 

procedures that, when implemented properly, will help ensure the safety and health of field crew 

members. A copy of this manual is provided to the field crew and may be downloaded from 

http://water.usgs.gov/owq/FieldManual/Chap9/content.html. Topics addressed in the USGS 

document include: 

 

• General references for federal policies and Department of Interior (DOI) safety 

guidelines 

• Safety policies you are required to know and follow under the Occupational Safety 

and Health Act (OSHA), Environmental Protection Agency (EPA), and Department 

of Transportation (DOT) 

• Understanding and implementing a job hazard analysis (JHA) 

• Requirements related to use of personal protective equipment (PPE) on the job, 

• Safety training and certification requirements 

• Safety issues associated with transportation and operation of vehicles (road vehicles 

and trailers, watercraft, aircraft, etc.) used to reach sampling sites 

• Surface water activities (e.g., wading, working from bridges, boats and cableways, 

etc.) 

• Working around machinery, pumps, and other equipment 

• Proper use, handling, transport, storage, and disposal of chemicals 

• Handling of contaminated water and limiting exposure to yourself and others 

• Environmental conditions caused by extremes in temperature; sun exposure; threats 

posed by storms, floods, fire, snow, ice, and various animals and plants 

In addition to consulting the USGS manual, the field crew should contact individual park’s 

safety officers or resource managers for information on park radio safety procedures and local 

problems and issues, such as dangerous or nuisance animals (e.g., black bears at VOYA, red fox 

at ISRO), insect-and tick-borne diseases (e.g., Lyme disease, encephalitis, West Nile disease), 

and other issues specific to each park. 

2.3.2 Basic Safety Preparation 

Basic preparations should become routine before every sampling activity. At a minimum, 

complete a trip plan for each field trip, and leave it at a designated location in the office. The trip 

plan should include the following information: 

• Field trip participants, including guests and observers, with emergency contact 

information 

• Departure and expected return time(s) and date(s) 

• Hotel and campground contact information (for overnight trips) 

• Basic itinerary, including where and when sampling will occur 

• Phone numbers for cellular phones or radio frequencies 

Field work should be done in pairs. Always carry a park radio and if service exists, a cellular 

telephone. Carry basic safety equipment, including first aid kit, flashlight, boots, rain gear, 

antibacterial soap or hand cleaner, matches or lighter, etc. Be aware of changing weather 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #2, page 5

conditions and the potential for storms. Be aware of potential hazards at a monitoring site. Carry 

general safety information in each vehicle or boat, including: 

• Material Safety Data Sheets (MSDS) for chemicals used in the field 

• Basic first aid protocols 

• Emergency phone numbers 

• Locations of emergency facilities (hospitals, police and fire departments, U.S. Coast 

Guard) 

• Maps of the park, surrounding area, and nearest city 

Job hazard analyses (JHAs), prepared by the project manager, will be discussed with field 

personnel prior to the field season. The JHAs will cover such topics as hiking and portaging, 

boating and sampling from a boat/canoe, lab safety, driving vehicles, and stinging insects and 

poisonous plants. 

2.3.3 Medical Forms and Safety Equipment Checklists 

The following pages contain medical forms and equipment checklists for field personnel 

(adapted from Lane and Fay 1997). Prior to the field season, complete as much of the medical 

information as possible. Confirm all contact information annually. Medical information sheets 

should be completed for each individual venturing into the field. 

Checklists are helpful for ensuring that personnel have the appropriate safety equipment 

available during field trips. Field crew members should consider their specific needs and should 

customize the checklists as necessary. The field crew and project manager will discuss the 

checklists and determine which items are necessary. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #2, page 6

Emergency Contact Form for: (name) 

Emergency contacts 

#1 Name: __________________________Relationship:___________________________ 

Phone: (home) (work) ______________________________________________________ 

 

#2 Name: __________________________Relationship:___________________________ 

Phone: (home) (work)______________________________________________________

Great Lakes Network Contacts 

Network Office 715-682-0631 x25 Mississippi NRRA ____________________ 

Apostle Islands NL ___________________ Pictured Rocks NL ____________________ 

Grand Portage NM ___________________ St. Croix NSR________________________ 

Indiana Dunes NL_____________________ Sleeping Bear Dunes NL _______________ 

Isle Royale NP _______________________ Voyageurs NP________________________ 

Local emergency contacts (or call 911) 

Hospital Phone: __________________________________________________________ 

Address: ________________________________________________________________ 

Other medical facility (24-hour care) Phone:____________________________________ 

Address:________________________________________________________________ 

Police___________________________________________________________________ 

Fire____________________________________________________________________ 

Utility__________________________________________________________________ 

Health Information Centers 

Center for Disease Control__________________________________________________ 

Information Hotline: ______________________________________________________ 

Other___________________________________________________________________ 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #2, page 7

Medical Information Form (retain in office) 

Employee name: ____________________________ Home phone: _________________ 

Treatment preference: medical _____________ other (specify) ____________________ 

Doctor: _________________________________ Phone: _________________________ 

Other emergency contact: ___________________________ Phone:________________ 

Allergies and other 

medical conditions Medications being taken Medications to avoid 

 

 

 

Relevant medical history: 

Special instructions: 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #2, page 8

General Safety Equipment Checklist 

√ Basic Safety Equipment Checklist 

 Waders, hip boots, rubber knee boots 

 Personal floatation device (PFD) 

 First aid kit 

 Fire extinguisher 

 Flashlight and spare batteries 

 Park radio and cellular phone 

 Rain gear 

 Hat, sun screen, and sunglasses 

 Drinking water or sports drinks 

 Safety cones, orange safety vest (working on bridges) 

 Tool box with basic tools 

 Antibacterial soap or hand cleaner 

 Spill kits (for preservatives) 

 Material Safety Data Sheets (MSDS) for preservatives 

 Hand-held eye wash unit 

 Protective goggles 

 Container to carry preservatives 

 List of emergency phone numbers and office contacts 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #2, page 9

Personal Protective Equipment Checklists

Personal Protective Equipment (PPE) must be selected based on the hazards likely to be 

encountered. The Great Lakes Network is required to supply appropriate PPE, and field 

personnel are required to use it. 

√ Chemical and disease protection 

 Aprons 

 Eye/Face splash guards 

 Gloves (vinyl and/or latex or nitrile) 

 Protective suits 

 Respirators (certification required for use) 

√ Weather and UV protection 

 Boots 

 Fluids (e.g., water, sports drinks) 

 Hat with a brim 

 Insect repellent 

 Rain gear 

 Sunglasses 

 Sunscreen 

 Temperature-modifying clothing 

 Work gloves 

√ Flotation and reflective protection 

 Orange flotation vests and jackets 

 Safety harness 

√ Protection for working around boat motors 

 Hearing protection 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #2, page 10

Checklists for Vehicles and Vehicular Laboratories 

√ Chemical protection and storage 

 Chemical spill kit 

 Eye wash kit (replace old or expired wash solution) 

 Material Safety Data Sheets (MSDS) 

 Chemical reagents (stored in appropriate area) 

 Flammable solvents (stored in appropriate dedicated area) 

 Pressurized gases (stored in appropriate area) 

√ Communications and instructions 

 Field folder (including maps, emergency phone numbers for medical facilities, 

office contacts, family contacts) 

 Cellular phone/park radio (check that the service is operational for the area to be 

traveled) 

√ First aid and protective equipment 

 Complete change of clothes (stored in dry area) 

 Fire extinguisher (safely secured) 

 First aid kit and manual (check for missing or old, expired items and replace if 

necessary) 

 Orange reflective vest 

√ Miscellaneous equipment 

 Bungie cords (to secure loose articles) 

 District flood plan (most current version) 

 Flagging 

 Flares 

 Flashlight (including fresh batteries) 

 Flexible hose (to vent exhaust away from vehicle) 

 Safety cones 

 Tool kit 

 U.S. Geological Survey TWRI Book 9 Chapter A9. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #2, page 11

Watercraft Checklists 

√ Instructions and navigation 

 Field folder, with sampling plans 

 Charts and maps 

 GPS unit 

 Compass 

 Depth finder 

 Dead-man’s switch 

 Navigation lights 

 Ring buoy with line 

√ Distress and external communication 

 Radio (VHF, AM, FM, and WEATHER) 

 Special lighting/flagging (if boat activities might pose a hazard to the public, such as tag 

line measurements) 

 Visual distress signals (Coast Guard approved) 

 Whistles or horns 

 Type IV throwable rescue device 

 Personal flotation devices for each passenger (Coast Guard approved) 

 Anchor and lines (spare) 

 Bucket for use as a bailer 

 Paddle (extra paddle for each canoe or rowboat) 

 First aid kit (Coast Guard approved) 

 Flashlights and batteries 

 Fire extinguishers 

 Spare parts (anchor, fuel, propeller, extra lines, cotter pin) 

 Tool and repair kits 

 Extra clothes (hat, foul-weather gear) 

 Food and water 

 Sunscreen 

 Conversion factors and abbreviations 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #2, page 12

2.4 Literature Cited 

Lane, S.L., and R.G. Fay. 1997. Ch A9: Safety in field activities. in National field manual for the 

collection of water-quality data: U.S. Geological Survey techniques of water-resources 

investigations, Book 9. Available from: <http://pubs.water.usgs.gov/twri9A9/>. 

O’Ney, S. E.. 2005. Standard operating procedure #3: Safety and health, Version 1.0. in

Regulatory water quality monitoring protocol, Version 1.0, Appendix E. Bozeman (MT): 

National Park Service, Greater Yellowstone Network. 

Water on the Web (WOW). 2004. Monitoring Minnesota lakes on the internet and training water 

science technicians for the future - A national on-line curriculum using advanced 

technologies and real-time data. University of Minnesota-Duluth, Duluth, Minnesota. 

(http://waterontheweb.org/curricula). 
Standard Operating Procedure #3: 

Using the Global Positioning System 

Version 1.0 

In Large Rivers Water Quality Monitoring Protocol 

Prepared by 

David VanderMeulen and Mark Hart 

National Park Service 

Great Lakes Inventory and Monitoring Network 

2800 Lake Shore Drive East 

Ashland, Wisconsin 54806 

david_vandermeulen@nps.gov 

 

August 2008 

Suggested citation: VanderMeulen, D., and M. Hart. 2008. Standard operating procedure #3: 

Using the Global Positioning System. In Magdalene, S, D.R. Engstrom, and J. Elias. 2008. Large 

rivers water quality monitoring protocol, Version 1.0. National Park Service, Great Lakes 

Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/060. National Park Service, Fort 

Collins, Colorado. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #3, page ii

Contents 

 Page

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

3.0 Introduction..........................................................................................................................1 

3.1 Role of GPS in Water Quality Monitoring on Large Rivers ...............................................2 

 

3.2 Using Mapping-Grade GPS Units .......................................................................................2 

 3.2.1 Data Dictionaries ........................................................................................................3 

 3.2.2 GPS Settings ...............................................................................................................3 

 3.2.3 Data Collection ...........................................................................................................6 

 3.2.4 Data Processing...........................................................................................................8 

3.3 Using Recreational-Grade GPS Units..................................................................................9 

 3.3.1 Planning ......................................................................................................................9 

 3.3.2 Data Collection .........................................................................................................10 

 3.3.3 Data Processing.........................................................................................................10 

3.4 Metadata.............................................................................................................................10 

3.5 GPS and NPSTORET ........................................................................................................11

3.6 Quality Assurance/Quality Control....................................................................................11 

3.7 Literature Cited ..................................................................................................................12 

Appendix A....................................................................................................................................13 

Tables 

 Page 

Table 1. GPS receiver settings, definitions, and standards for use at GLKN parks ................................... 4 

Table 2. Coordinate system settings for Great Lakes Network parks..............................................5 

Table 3. Recommended fields to be exported in addition to GPS features .....................................8 

Figures 

 Page 

Figure 1. Examples of GPS point and line features data collection.................................................7 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #3, page iii

Revision History Log 

 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project manager must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the header of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log: 

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #3, page iv

Acknowledgements 

Major portions of this SOP have been adopted from the GLKN GPS Field Data Collection 

Guide. The guide was originally published as Appendix K to the Great Lakes Inventory and 

Monitoring Data Management Plan (Hart and Gafvert 2005). Appendix A of this SOP was also 

adopted from that document, and contains a summary discussion of the general types of GPS 

units available, as well as definitions of terms commonly associated with use of GPS units. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #3, page 1

3.0 Introduction 

This standard operating procedure (SOP) provides guidance on some of the more common 

operations associated with Global Positioning System (GPS) units. Although most GPS units are 

capable of multiple functions, only those operations relevant to the protocol established to 

monitor water quality on large rivers (Magdalene et al. 2008) are discussed. 

GPS units currently (2007) used by water quality monitoring staff are the Trimble GeoXT and 

Garmin 76S. The Trimble GeoXT is an example of a mapping-grade GPS unit, while the Garmin 

76S is an example of a recreational-grade unit. Mapping-grade units record data with location 

accuracy ranging from sub-meter to less than five meters. Recreational-grade units generally are 

not as accurate, with spatial accuracy less than 15 meters. Mapping-grade units have greater 

ability to capture spatially referenced metadata (i.e., attributes) than recreational-grade GPS 

units. A detailed discussion of these types of GPS units can be found in Appendix A. 

As of 2007, software pertinent to the use of these GPS units includes: 

• TerraSync (Trimble GeoXT) – single table forms software 

• ESRI ArcPad – multi-table mobile GIS/database software 

• GPS Pathfinder Office 3.xx (Trimble GeoXT) – desktop GPS processing software 

• ESRI ArcGIS 9.x (Trimble GeoXT or Garmin 76S) – desktop GIS software 

• Minnesota Department of Natural Resources Garmin Extension for ArcView (Garmin 

76S) (i.e., DNR_Garmin) 

• NPSTORET software, Version 1.xx – NPS database for water quality data (refer to SOP 

#8, Data Entry and Management). 

Due to the rapid development of commercial software and hardware capabilities, it is likely that 

other GPS units or software will be utilized in the future. Therefore, this SOP is meant to act as a 

working document that is updated periodically as new hard-software becomes available. 

Although nomenclature may differ depending on what hard-software is utilized, this document 

should provide sufficient guidance on the general process of data collection using GPS tools until 

the SOP is revised. It is strongly recommended that water quality monitoring staff obtain unitspecific GPS training prior to deploying in the field. The training should include hands-on use, 

and should be designed to test all appropriate functions and operations prior to going out into the 

field. 

Additionally, this SOP is not intended to be exhaustive or simply a regurgitation of operating 

manuals, but a document that might be carried into the field or periodically reviewed by field 

technicians and project leaders. Although some of the information in this SOP is specific to the 

water quality monitoring effort by GLKN, much of the text contained herein is applicable to 

other data collection efforts by GLKN staff. The objective of this document is to summarize GPS 

use guidelines applicable to the water quality monitoring efforts for large rivers at GLKN partner 

parks. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #3, page 2

3.1 Role of GPS in Water Quality Monitoring on Large Rivers 

GPS units are primarily used in the following ways to support water quality monitoring on large 

rivers: 

1) When an area of the river to be monitored is selected, permanent markers on each river 

bank may be established to delineate a river cross-section at the monitoring site (or 

stations). GPS units are used to record the location of each marker and the heading, from 

right bank to left bank, between markers. Sampling personnel on subsequent visits should 

measure along the same cross-section. A detailed discussion of how sites are selected and 

established on rivers is discussed in SOP #4, Site Establishment. It is recommended that a 

mapping-grade GPS unit be used to obtain a higher precision location during site 

establishment. These coordinates should then be used as the master or default location for 

the site. 

2) For water quality monitoring on large rivers, navigating to and sampling at the position 

locations of monitoring stations is accomplished through a combination of: 

• Using GPS units to navigate to previously established GPS point locations 

• Using hardcopy topographic maps and written notes with site descriptions 

• Comparing digital photos taken during site establishment with observer ocular 

estimates 

• Field experience of NPS staff conducting the monitoring 

3) Accurate station location descriptions must be recorded and carefully followed by 

sampling personnel on subsequent field visits for water quality monitoring. Therefore, 

once on station, GPS equipment is used to obtain the station’s coordinates, which allows 

the user to spatially reference water quality monitoring data to specific geo-referenced 

locations for each sampling event. 

Additional uses of the GPS units may develop over time if protocols change or other needs are 

identified. For example, the Great Lakes Network currently promotes the use of electronic data 

logging equipment to enhance data quality and simplify data management. Many water quality 

parameters (e.g., pH) are now primarily recorded with electronic data logging equipment, while 

others (Secchi disk depth, names of observers, etc.) are logged on hardcopy only. Therefore, 

GPS units capable of logging more information other than just waypoints (e.g., Trimble GeoXT) 

could be programmed to allow for electronic recording of these parameters. The next two 

sections of this SOP will outline some of the more common and pertinent functions associated 

with mapping and recreational-grade GPS units, which are the types of units currently used by 

GLKN staff for water quality monitoring. 

3.2 Using Mapping-Grade GPS Units 

All mapping-grade GPS users should become familiar with GLKN GPS collection procedures 

and relevant manufacturer’s user guides and operating manuals before GPS operation. For 

example, prior to using a Trimble GeoXT (mapping-grade) GPS unit, the following documents 

should be reviewed: 
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• Appendix A of this SOP 

• GeoExplorer CE Series: Getting Started Guide 

• GPS Mapping for GIS with TerraSync and GeoExplorer CE Series or TerraSync 

Operation Guide v2.4x 

• Basic GPS Data Capture Using TerraSync: A Quick Start Guide 

Mapping-grade GPS units provide the user with a variety of tools for field data collection. 

GLKN encourages the use of these units for most projects. These units can be used to acquire 

spatial data related to points, lines, and polygons along with associated, user defined, tabular 

attributes. Careful forethought and advanced planning are required to take advantage of these 

capabilities long before data collection begins. 

3.2.1 Data Dictionaries 

TerraSync software on mapping-grade GPS units is capable of using data dictionaries. Data 

dictionaries define the structure and rules to store attribute information about the feature being 

mapped and are customized for each project. GLKN data management personnel should be 

directly involved in the creation of data dictionaries. Basic steps include: 

1) Identify the features to be mapped. These features are real-world physical locations of 

objects (e.g., a water quality monitoring station) that are categorized as point, line, or 

polygon features. 

2) Identify the attributes to be collected for each feature while in the field and create a data 

dictionary. Part of this process is assigning a unique identifier to each feature. (For 

example, if a survey plot is mapped as both a point and a polygon, one feature should be 

named plotname_poly and the other plotname_pt.) 

3) Implement and test the data dictionary. Field staff should conduct a complete trial run for 

newly-created data dictionaries before beginning field work. Corrections and refinements 

are inevitable after such a trial. 

Because most of the data for water quality monitoring on large rivers are recorded by electronic 

sampling equipment, there has not been much incentive to utilize data dictionaries. However, as 

discussed earlier, it is possible that the few parameters not currently logged electronically could 

be incorporated into a data dictionary and recorded. As stated above, it is highly recommended 

that GLKN data management personnel be involved in this process, and that once created, the 

data dictionary only be altered with permission from data management personnel. This will 

reduce the potential for confusion and mistakes when data are processed at the end of the field 

season. 

3.2.2 GPS Settings 

Positional accuracy of GPS data can be affected by several factors that can be monitored and 

recorded with mapping-grade GPS units. Table 1 lists these factors, their definitions, and the 

standard settings for GLKN field work. All spatial data collected shall be analyzed for spatial 

accuracy and shall meet or exceed the National Map Accuracy Standards (Table 1 in Appendix 

A, and http://mapping.usgs.gov/standards/). Table 2 indicates the coordinate system settings for 

data collection in GLKN parks. 
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Table 1. GPS receiver settings, definitions, and standards for use at GLKN parks. 

Setting Name Definition GLKN Setting Standard 

Almanac File containing estimated position of 

satellites, time corrections, and 

atmospheric delay parameters 

Acquired automatically by GPS 

unit or from online sources within 

10 days prior to GPS field work 

Altitude reference Ellipsoid model Height above Ellipsoid (HAE) 

(preferred) or Mean Sea Level: if 

MSL is used, indicate Geoid Model 

Antenna height GPS antenna height above the 

ground 

Variable, usually 1.0 meters for 

handheld and 1.5 m for backpack 

Datum Geodetic model designed to fit a 

point on the earth’s surface to an 

ellipsoid 

NAD 83 (CONUS) [preferred] 

WGS 84 [GPS default, as fallback] 

NAD 83 (CONUS) (CORS 96) [for 

H-Star use with GeoXH Trimble 

GPS Unit] 

Elevation mask The minimum angle above the 

horizon at which a GPS receiver 

will track a satellite 

15 degrees 

Feature types Geometry of spatial data GIS native formats; point, line and 

polygon are preferred 

Logging interval Time interval between the recording 

of individual GPS fixes 

Points: 1 second 

Lines and Polygons: 5 seconds, but 

1 second in some circumstances 

Minimum fixes for point 

positions 

Number of GPS fixes that are used 

to calculate a single position for a 

point feature 

50 fixes (120 points in the case of 

GeoXH) 

Mode 2-dimensional for horizontal 

positions and 3-dimensional with an 

elevation position 

3-dimensional (4 satellite 

minimum) 

PDOP mask Positional Dilution of Precision, a 

GPS quality estimate based on 

satellite geometry 

6.0 or less 

Real-time settings GPS unit may be capable of 

performing differential correction of 

data during collection 

Select Integrated WAAS (unless 

using H-star, e.g., XH unit); setting 

will be ‘auto’ or ‘on’ 

Satellite vehicles Number of satellites used for 

position fixes 

4 minimum 

SNR mask Signal-to-Noise ratio is a measure 

of the satellite signal relative to 

background noise 

4.0 minimum, 6.0 or greater 

preferred 

Unit of measure Linear unit of measure Meter (metric) 
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Table 2. Coordinate system settings for Great Lakes Network parks. Bold font indicates parks 

where water quality monitoring on large rivers will take place. 

GPS signals are received in the WGS84 datum. Processing and transformation of the positional 

information to other datums can take place internally in the GPS unit or in software, either the 

GPS data processing software (see below) or in GIS software. GPS data that will receive no postprocessing differential correction, unlikely with a mapping grade receiver, can be collected in 

native WGS84 or NAD83 (CONUS), and ensuring that the datum used is recorded in the 

metadata. More likely with a mapping grade receiver, the GPS data will be differentially 

corrected after collection using data from one or more reference base stations. Data on the GPS 

unit should be collected in the same datum as the data are output from the reference base 

stations. The majority of public base stations in the US are part of the National Geodetic Survey's 

Continuously Operating Reference Station (CORS) network; and output information in the 

NAD83 (CONUS) CORS datum. Setting the GPS unit to record data in NAD83 (CONUS) 

CORS datum will result in the most accurate spatial information when differentially corrected 

against a CORS base station. A very high precision mapping grade unit may use H-Star 

technology, which requires post collection differential correction; using the NAD83 (CONUS) 

CORS datum and no real-time correction (WAAS) on the GPS unit, and correcting against a 

group of CORS base stations is necessary to realize the maximum accuracy from an H-Star 

receiver. 

Before beginning data collection, the GLKN data management staff or the GPS user should 

complete some mission planning tasks. If high accuracy fixes are desired and there is some 

flexibility in scheduling of a field data collection mission, the user should complete a satellite 

survey to determine the best timing of the mission, usually when the most satellites are visible 

and in the best geometry. Software, such as Trimble’s Quick Plan (also included in Pathfinder 

Office) can be used to look for time windows that should offer the lowest PDOP readings, and 

thus the highest positional accuracy. 

If a project requires navigation to preset locations or waypoints, this information must be preloaded onto the GPS hardware before starting a field data collection mission, unless the locations 

have been previously stored on the GPS. Having printed copies of topographic maps with 

waypoints marked is a good backup and can maximize field time and efficiency when navigating 

between waypoints and sites. Some of the sampling stations on large rivers are located near 

unique shoreline features (e.g., rock outcrop or bridge), which are annotated on topographic 

Park UTM Zone Datum 

APIS 15 NAD 1983 (Conus) 

GRPO 16 NAD 1983 (Conus) 

INDU 16 NAD 1983 (Conus) 

ISRO 16 NAD 1983 (Conus) 

MISS 15 NAD 1983 (Conus) 

PIRO 16 NAD 1983 (Conus) 

SACN 15 NAD 1983 (Conus) 

SLBE 16 NAD 1983 (Conus) 

VOYA 15 NAD 1983 (Conus) 
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maps. Detailed descriptions and photographs of the shoreline are also used to navigate to 

designated sampling sites. 

Many mapping-grade GPS units have the capability of storing and displaying background maps 

or GIS layers, which can be very helpful when navigating in the field. For example, topographic 

maps of the St. Croix River, which also show water quality sampling stations, can be used with 

GPS units. The GLKN data management staff can support preparation of these background 

layers and, if necessary, assist in loading them onto the GPS hardware. 

GPS units create files to store data during a field session using a prefix and date-time stamp as 

file names. For example: 

RMMDDHHx 

R – Unit Prefix 

MM – Month 

DD – Day 

HH – Hour 

X – a, b, c, etc., the order files are created within an hour 

If multiple GPS units are used for a project, a unique prefix (letter) should be assigned to each 

unit, which will ensure that downloaded files for each unit contain a unique identifier within the 

filename. For example, with three GPS units, the unique letters for the units could be N, G, and 

A. Those letters would serve as a prefix for the file n (e.g., N102715A, G102715A, and 

A102715A would indicate units N, G, and A, October 27, 15 hour, A first in hour). In addition, if 

a data dictionary is used, and entry of the observer’s name or initials is not an option in the 

dictionary, then the observer’s name or initials should be included in the file name. 

Each user should be familiar with the capabilities of the GPS hardware and field computers. If 

possible, water quality monitoring staff should receive hands-on instruction from someone 

familiar with the equipment. At a minimum, the equipment user guides and operator’s manuals 

should be reviewed, and the operator should test the functions s/he intends to use. 

It is extremely important that each user become familiar with the battery power and memory 

capabilities of the GPS units. All units have limited battery and memory resources; these features 

should be thoroughly tested to gain an understanding of the power and memory limitations of the 

GPS units before being deployed in the field. It is possible to power or recharge these units from 

a DC power source, such as a vehicle power outlet. 

3.2.3 Data Collection

Data collection should be performed using an approved data dictionary or database for the 

protocol, if applicable. Moreover, users should be mindful of the following concepts: 

• If using a GPS unit that gives an approximate 5m horizontal accuracy, the user cannot 

map anything as a polygon that is less than 4 to 6m in width or diameter. Such objects 

must be captured as point features. 

• If a GPS user is collecting a line or polygon feature and then stops moving, the GPS unit 

will continue to collect data (Figure 1, examples 1 and 2). Users need to be familiar with 
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the Pause/Resume toggle key and use it liberally. This technique greatly improves 

subsequent data quality and reduces the need for time-consuming spatial editing. 

• Another way to avoid errors is to collect point features that represent the beginning and 

end points of a line transect (Figure 1, examples 3 and 4). Having these reference point 

locations will mean easier editing of any zig-zagging line features. 

Figure 1. Examples of GPS point and line features data collection. 

 

Mapping-grade GPS units have additional features that aid in data collection. These include: 

• Nested Feature – Allows user to collect a point while collecting a line or polygon feature. 

For example, while surveying potential amphibian habitat along a stream (line feature), 

the user can pause the line feature, take a point for a specific observation, then resume the 

line feature collection. 

• Offset Feature – Allows user to collect a feature when topography is such that getting 

next to or over the feature is impossible. For example, a GPS line could be collected 

while taking a horizontal zooplankton tow off the side of a boat. 
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• Between-feature Positions – the GPS unit collects positions without any feature or 

attribute data. This feature is useful for tracking areas traveled during a day. For example, 

while surveying for presence or absence of invasive plants, a user could collect data on 

the area surveyed in addition to locations of specific plants found. 

3.2.4 Data Processing 

When data collection is complete for the day or round of sampling, data are downloaded from 

the GPS unit to a computer. For Trimble GPS units, the proprietary software Pathfinder Office 

(or the GPS Analyst extension) is used to download, differentially correct, and then export the 

data to a GIS format. [Note: Trimble Pathfinder Office and GPS Analyst are relatively 

expensive. However, Trimble also offers a free data transfer utility to download data from the 

GPS units to a Windows-based PC]. Differential correction is a post-processing procedure to 

improve upon raw GPS positions using base station data. Base stations consist of a GPS antenna 

and receiver positioned at a known location specifically to collect data from satellites. The 

distance between the base station(s) and the remote GPS receiver should be kept to a minimum. 

 

Differential correction should be conducted on all GPS data collected, even if data were 

collected using the real-time collection feature. Once the data are differentially corrected, they 

can be verified and edited. Unintentional features can be deleted and attributes can be reviewed. 

The last step in processing data is exporting the dataset to GIS (ArcGIS or ArcView). Depending 

on the software used for this process, newly created files generated when exporting data are often 

assigned generic names. For example, if Pathfinder Office is used to export a file named 

‘VOYA2007.cor’ (.cor denotes that the file has already been differentially corrected) that only 

contains point features, the exported file will be named ‘point_ge.shp’. Great care should be 

taken to not overwrite this file when exporting other data, as the software will continue to use 

this generic naming convention the next time it is used. In addition, during the export process, 

the coordinate system to which the data will be exported to should be verified (Table 2). 

Additional data attributes can be included in the data exports. Data attributes recommended by 

GLKN are listed in Table 3. 

 

Table 3. Recommended fields to be exported in addition to GPS features. 

All Features Point Features Line Features Area Features 

PDOP Height Length (2D) Area (2D) 

Correction status Position Length (3D) Perimeter (2D) 

Receiver type Perimeter (3D) 

Date recorded 

Data file name 

Total positions 

Data dictionary name 

 

Managing the incoming GPS data can be a challenge, especially if there are multiple units per 

project. Common practices used by GLKN include: 

 
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• Download all data to a computer or network drive that is regularly backed up. 

• Keep GPS data and GIS data separate through electronic file management. 

• Directories and files names should not contain non-alpha-numeric characters and/or 

spaces (except underscores). 

• Keep GPS data in well-organized directories (see Hart and Gafvert [2005], GLKN Data 

Management Plan, for more details). 

 

At the end of a project, all data and background files should be removed from the GPS unit to 

free available memory. Data files should not be left on a unit if they have been properly 

downloaded and verified. In addition, some GPS units require their batteries to be re-charged 

periodically. Failure to do so can cause the GPS unit batteries to discharge completely, and may 

cause some files and software to be deleted. 

 

Additional information can be found at http://www.nps.gov/gis/gps/gps4gis/, which describes the 

steps outlined here in greater detail. 

3.3 Using Recreational-Grade GPS Units 

Recreational-grade GPS units can be used to acquire location information (generally points) 

when spatial accuracy is not paramount to the project. Recreational GPS units do not have data 

dictionaries for storing attribute information with the point location. However, using a 

recreational-grade unit to capture a waypoint at each sampling site is a reliable means to verify 

the correct sampling site has been reached, even if a GPS location is not needed. 

As with mapping-grade GPS units, personnel that employ recreational-grade GPS units should 

become familiar with GLKN GPS collection procedures and relevant manufacturer’s user guides 

and operating manuals before GPS operation. For example, prior to using a Garmin 76S 

(recreational-grade) GPS unit, the following documents should be reviewed: 

• Appendix A of this SOP 

• GPSMAP 76S Quick Start Guide 

• GPSMAP 76S Owner’s Manual and Reference Guide 

• Garmin MapSourceTM User’s Manual and Reference Guide 

3.3.1 Planning 

If a recreational-grade GPS meets the criteria of the project, the unit chosen must have the 

capability of downloading collected data to a personal computer. Downloading data is usually 

accomplished with a parallel or USB cable connection. 

 

Much of the data collected by GPS will eventually reside in a relational database. Each GPS 

feature collected should contain a unique identifier that relates the feature to an associated record 

in a database. For water quality monitoring on large rivers, the records associated with each GPS 

feature will consist primarily of water quality parameters. Since recreational GPS units have only 

one text field for input, careful consideration should be given to the use of this field and the 

design of unique identifiers. GLKN data management and GIS staff can assist in creating unique 

IDs on a project by project basis. 
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3.3.2 Data Collection 

Location data are captured by recreational-grade GPS units as waypoints. When taking a 

waypoint, enter the site ID or site designation in the text field provided. It is also good practice to 

collect reference points at regular intervals. These reference point positions should be taken at 

known locations (e.g., trailheads, parking lots, stream confluences) that can later be used in GIS 

to check the accuracy of waypoint data. 

 

If navigation to preset waypoints is applicable to a project, the waypoints must be loaded onto 

the GPS unit before departure to the field. Some recreational grade GPS units have the ability to 

store and display topographic maps, which can aid in navigation. Printed topographic maps of 

the waypoint locations can also be used to maximize field time and efficiently navigate between 

waypoints. 

 

3.3.3 Data Processing 

Data should be downloaded from GPS units once a day or after each field session. The DNR 

Garmin freeware product: 

(http://www.dnr.state.mn.us/mis/gis/tools/arcview/index.html ) can be used to download data 

from Garmin GPS units. Data should be downloaded both as a text file and a shapefile. Each file 

name should include the download date. Points should be checked for reasonable spatial 

accuracy and errors. Subsequent downloads should be error-checked in the same manner. When 

data collection is finished, all files should be compiled into one spatial file, and along with the 

raw downloads, should be saved to the appropriate location on Great Lakes Network servers 

(refer to SOP #8, Data Entry and Management for more detail). 

3.4 Metadata 

Regardless of the type of GPS unit used to collect data, all resulting GIS datasets need to have 

information documenting how the GPS data were collected. NPS requires that FGDC (Federal 

Geographic Data Committee, www.fgdc.gov/index.html ) compliant metadata be written for all 

geospatial layers created (Executive Order 12906). 

 

Until final FGDC metadata is written, the data collection and management process is incomplete. 

Tracking GPS projects depends on the complexity of the project, how many participants, length 

of project etc. Documentation can be a simple ‘readme’ text file, or a detailed daily log. 

 

The Great Lakes Network recommends formal metadata be written by the data collectors, as they 

are the ones familiar with the project and resulting data. However, Network data management 

and GIS staff are usually the ones documenting someone else’s work. Chapter 7 of the GLKN 

Data Management Plan (Hart and Gafvert 2005) includes a detailed discussion of metadata 

procedures. At a minimum, the following details should be documented to facilitate final FGDC 

metadata: 

• Name of project 

• Name(s) of data collectors 

• EHE/EPE or maximum PDOP (using 4 satellites) 

• Coordinate system (projection, datum, and zone) 
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• Type (or types) of GPS units used 

• The range of field collection dates 

• Name of base station(s) used for differential correction 

• Name and version of software used for downloading 

• Any major editing performed on the raw data (e.g., moving of points) 

• All versions of data dictionaries used 

3.5 GPS and NPSTORET 

Water quality data, including chemical, physical, and biological data, are managed according to 

guidelines from the NPS Water Resources Division. These guidelines include using the 

NPSTORET desktop database application to help manage data entry, documentation, and 

transfer. The Network oversees the use of NPSTORET according to the Network’s water quality 

monitoring protocols and ensures the content is transferred at least annually to NPS Water 

Resource Division for upload to the EPA STORET (STOrage and RETrieval) database. 

NPSTORET requires that every water quality monitoring station location must have an assigned 

latitude and longitude coordinate. Also, the horizontal datum to which these coordinates are 

referenced (typically North American Datum 1983 or World Geodetic System 1984) and the 

method by which they were obtained (GPS, map interpolation, etc.) must be provided. Therefore, 

the GLKN project leader for monitoring water quality on large rivers and the GLKN data 

manager collaborate in organizing monitoring station coordinates in an acceptable format (e.g., 

Excel spreadsheet or Access database) to be imported to the NPSTORET database. A detailed 

discussion on using the NPSTORET database is found in SOP #8, Data Entry and Management.

3.6 Quality Assurance/Quality Control

Long-term monitoring is only useful if users have confidence in the data. Efforts to detect trends 

and patterns in ecosystem processes require high-quality, well-documented data that minimize 

error and bias. Data of inconsistent or poor quality can result in loss of sensitivity and lead to 

incorrect interpretations and conclusions. 

NPS Director’s Order #11B: Ensuring Quality of Information Disseminated by the National Park 

Service (www.nps.gov/policy/DOrders/11B-final.htm) specifies that information produced by 

the NPS must be of the highest quality and based on reliable data sources that are accurate, 

timely, and representative of the most current information available. Therefore, GLKN will 

establish and document procedures for quality assurance (QA) and quality control (QC) to 

identify and reduce the frequency and significance of errors at all stages in the data life cycle 

(see SOPs #8 and #12 for details on data management and QA/QC, respectively). Under these 

procedures, the progression from raw data to verified data to validated data implies increasing 

confidence in the quality of those data. Quality assurance and quality control procedures will 

document internal and external review processes and include guidance for addressing problems 

with data quality. 

Examples of general of QA/QC practices include: 
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• Standardized field data collection forms 

• Use of field computers and automated data loggers 

• Proper calibration and maintenance of equipment 

• Training of field crew and data technicians 

• Database features such as built-in pick lists and range limits to reduce data entry errors 

• Automated error-checking routines 

Many of the standard operating procedures associated with the protocol for monitoring water 

quality in large rivers include a discussion of QA/QC as it relates to the protocol. Examples of 

QA/QC practices pertaining to use of GPS include: 

• Ensure that GPS-related software is periodically updated as it becomes available and has 

been tested. 

• Record location positions on field data forms as well as with the GPS unit. 

• For each monitoring station, compare location positions for different sampling events, 

including the position recorded during establishment of the monitoring station. This will 

allow for an assessment of position accuracy over time. 

• If data dictionaries are used with mapping-grade GPS units, ensure that the coordinates 

for the monitoring station match the other attributes recorded on the GPS unit for that 

monitoring station. 

• Check to see if the accuracy of the GPS unit meets or exceeds the National Map 

Accuracy Standards shown in Table 1 of Appendix A. 

• Ensure that the appropriate coordinate system is used when collecting and exporting data. 

• Use mapping software (e.g., Pathfinder Office or ArcGIS 9.x) to view waypoints (or 

features) overlaid on a geo-referenced air photo or topographical map to check for 

accuracy. 

• If applicable, check the accuracy of the attribute(s) recorded on a GPS unit by using 

mapping software (see bullet above) and look-up tables or in spreadsheets generated after 

post-processing is complete. 

A final report on data quality, including data collected by GPS, will be incorporated into the 

documentation for this project. Such documentation will include a listing of the specific methods 

used to assess data quality and an assessment of overall data quality prepared by the project 

manager. This is a necessary part of the data quality elements of the metadata file. 

3.7 Literature Cited 

Hart, M., and U. Gafvert, editors. 2005. Data management plan: Great Lakes Inventory 

and Monitoring Network. National Park Service Great Lakes Inventory and Monitoring 

Network Report. GLKN/2005/20. 

Magdalene, S., D.R. Engstrom, J. Elias. 2008. Large rivers water quality monitoring protocol, 

Version 1.0. National Park Service, Great Lakes Network, Ashland, Wisconsin. 

NPS/GLKN/NRR—2008/060. National Park Service, Fort Collins, Colorado.
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Appendix A

This appendix discusses the role of GPS in GLKN data management and provides an explanation 

of the types of GPS units that are available. The text is taken directly from the GLKN GPS Field 

Collection Guide, which can be found in its entirety in Appendix K of the Great Lakes Inventory 

and Monitoring Data Management Plan (Hart and Gafvert 2005). 

Introduction 

Over the past decade new tools have been developed to help researchers collect and manipulate 

data while in the field. Global Positioning System (GPS) is one such tool. GPS is currently a 

constellation of 28 US Department of Defense satellites (as of 2006) orbiting 11,000 miles above 

the Earth, making a complete orbit approximately every 12 hours, and transmitting signals to 

Earth at precisely the same time. The position and time information transmitted by these 

satellites is used by a GPS receiver to triangulate a location coordinate on the earth using three or 

more satellites. 

Role of GPS in GLKN Data Management 

Data collected using GPS-enabled equipment represents all or part of the acquisition stage of an 

information resources lifecycle that includes several other stages (see Section 5.4 in GLKN Data 

Management Plan). The process and methodology used for acquisition, planning, data collecting, 

and post-processing incorporate several aspects of data management, including quality 

assurance, data storage and organization, and data stewardship. To promote data quality and 

simplify data management, the Great Lakes Network expects to use electronic data logging 

equipment for some data acquisition. However, parallel or complementary use of hand written 

data sheets and field notes will remain important for data collection activities. 

Types of GPS Units 

At the most basic level GPS equipment can just consist of a GPS antenna and the associated 

signal processing circuitry. The antenna can be a standalone device, be incorporated in to a 

handheld unit, or be integrated into a larger electronic device, such as a personal data assistant 

(PDA), data logger, or portable computer. As technology evolves, the Great Lakes Network will 

continually try to use equipment which maximizes spatial accuracy; reduces hardware weight 

and user fatigue; and reduces database development, data manipulation, and transformation. 

There are three major types of GPS units that are based on the level of accuracy to which spatial 

data can be collected. Survey-grade GPS units are used for surveying tasks that require very high 

accuracy (1 cm or less). Mapping-grade units can map features from sub-meter to less than 5m 

accuracy, employing differential correction. Recreational-grade GPS units are sold primarily for 

outdoor sports and recreational activities. Accuracy using recreational GPS units ranges from 5 

to 30m. Most natural resource-related data collection requirements correspond to either the 

recreational-grade or mapping-grade. Figure 1 shows some of the major differences between 

these two types. 
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Deciding which type of unit to use is an essential part of project planning, and depends on the 

end product needed. Mapping-grade GPS units are recommended for most GLKN field work; 

however, for some projects recreational-grade units can meet a project’s accuracy requirements 

and reduce the cost of field operations. The choice of GPS unit should be made by the project 

manager after consulting with the GLKN data management and GIS staff. 

Figure 1. Differences between different grades of GPS units. 

All resulting GIS data layers need to meet or exceed the National Map Accuracy Standards for a 

1:24,000 product (NPS GIS Data Standards, 2002 

http://www.nps.gov/gis/data_info/standards.html). Table 1 provides the allowable horizontal 

accuracy for some common scales. 

Table 1. Map scales and allowable error 

Scale Allowable Error 

1:40,000 33.8 meters (111 feet) 

1:31,680 16.1 meters (53 feet) 

1:24,000 12.2 meters (40 feet) 

1:20,000 10.1 meters (33 feet) 

1:12,000 6.1 meters (20 feet) 

1:9,600 4.9 meters (16 feet) 

1:4,800 2.4 meters (8 feet) 

1:2,400 1.2 meters (4 feet) 

1:1,200 0.6 meters (2 feet) 
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Definitions 

 

Accuracy - The degree of conformance between the estimated or measured position, time, 

and/or velocity of a GPS receiver and its true time, position, and/or velocity as compared with a 

constant standard. 

 

Almanac -Data transmitted by a GPS satellite, which include orbit information on all the 

satellites, clock correction, and atmospheric delay parameters. The almanac is used to facilitate 

rapid satellite vehicle (SV) acquisition. The orbit information is a subset of the ephemeris data 

with reduced precision. 

 

Attribute – Tabular information about a specific feature. 

 

Base Station - GPS files collected continuously from community base stations, local base 

stations, or Continually Operating Reference Stations (CORS). Gathering base files will require 

an internet connection and software that dials into a server that houses the base station data 

collected at the same time of the rover. Data stored on these servers will not be available in realtime - hence this step is conducted after field collection. Trimble users would use the Differential 

Correction utility supplied in Pathfinder Office. 

 

Differential Correction - The merging of rover file data with base map data to correct position 

errors due to atmospheric interference. Autonomous data (rover) are collected in the field while 

base data are stored at the stationary base station. The two datasets are loaded into a postprocessing software package where corrections are applied. This process will reduce errors in the 

field collected data (the rover) by correlating and correcting for known errors recorded in the 

base file that has the same time tag. As distance between the rover and base file increase, there is 

degradation in post-processed accuracy. In general, a degradation of one part per million (1ppm) 

occurs as the distance between the base station and rover increases. For example, one millimeter 

of degradation occurs for every kilometer between base and rover. 

 

Datum (geodetic datum) – A mathematical model that is designed to fit a point on the earth’s 

surface to an ellipsoid. Commonly used datums are North American Datum (NAD) 1927, and 

NAD 1983, modeled to represent the North American continent. 

Feature - A feature is the spatial location of a physical object, or some event or phenomenon. 

Features are often referred to as graphic data in a GIS. Examples include a tree (point), road 

(line), or land parcel (polygon). 

FGDC - The Federal Geographic Data Committee is a 19 member interagency committee 

composed of representatives from the Executive Office of the President, Cabinet-level and 

independent agencies who develop policies, standards, and procedures for organizations to 

cooperatively produce and share geographic data. (www.fgdc.gov/index.html) 

Global Positioning Systems (GPS) – a constellation of a minimum of twenty-four satellite 

vehicles orbiting the earth approximately every twelve hours at an approximate pacing of sixty 

degrees, between 11,000 – 12,000 miles above the surface of the Earth 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #3, page 16

Lines – geographic term related to the scale that describe how a feature is drawn. Lines are linear 

measures of a feature (such as a line representing a trail) 

Mapping Grade – GPS receivers capable of attaining five meters of accuracy or better using 

differential correction. 

Metadata - Data about the data. Usually comes in the form of a text or html document with 

information on the dataset's quality, current projection, attributes, distribution and citation. In the 

National Park Service, this generally implies a file compliant to the FGDC Content Standard for 

Digital Geospatial Metadata. 

Multipath – error which occurs when a GPS signal sent from a satellite vehicle is bounced or 

redirected by an object, prior to reaching a GPS receiver. Multipath will cause the time it takes a 

GPS signal sent by a satellite vehicle to reach a GPS receiver to be inflated. This will cause 

inaccuracies in positions collected. 

Points – geographic term related to the scale that describe how a feature is drawn. Points are 

single dimensional features (such as a point representing a spring). 

Polygons - geographic term related to the scale that describe how a feature is drawn. Polygons 

have area associated with the feature (such as a circle representing a parking lot). 

Projection - A method of representing the earth's three-dimensional surface as a flat twodimensional surface. This normally involves a mathematical model that transforms the locations 

of features on the earth's surface to locations on a two-dimensional surface. 

Post Processing – utilizing base station data, GPS software, and data acquired by a GPS receiver 

in the field to gain an accurate fixed position. 

Triangulation - The process of determining the distance between points on the earth’s surface 

by dividing up a large area into a series of connected triangles, measuring a base line between 

two points, and then locating a third point by computing both the size of the angles made by lines 

from this point to each end of the base line and the lengths of these lines. 

Waypoint – a named 3 dimensional position on the earth’s surface, that is, having both a latitude 

and longitude. Waypoints are assigned to a fixed location in the field so it can be navigated to 

consistently and accurately through time. 
Standard Operating Procedure #4: 

Site Establishment 

Version 1.0 

In Large Rivers Water Quality Monitoring Protocol 

Prepared by 

Suzanne Magdalene and Daniel Engstrom 

St. Croix Watershed Research Station 

16910 152nd. St. North 

Marine on St. Croix, Minnesota 55047 

and 

Joan Elias (contact author) 

National Park Service 

Great Lakes Inventory and Monitoring Network 

2800 Lake Shore Drive East 

Ashland, Wisconsin 54806 

joan_elias@nps.gov 

August 2008 

Suggested citation: Magdalene S., D.R. Engstrom, and J. Elias J. 2008. Standard operating 

procedure #4: Site establishment. in Magdalene, S, D.R. Engstrom, and J. Elias. 2008. Large 

rivers water quality monitoring protocol, Version 1.0. National Park Service, Great Lakes 

Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/060. National Park Service, Fort 

Collins, Colorado.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #4, page ii 

Contents 

 Page

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

4.0 Introduction..........................................................................................................................1 

4.1 Establishing NPSTORET Project Files ...............................................................................1 

4.2 Selection of Proposed Monitoring Stations .........................................................................1 

4.3 Permission for Research ......................................................................................................1 

4.4 Location Reconnaissance and Assessment ..........................................................................1 

 4.4.1 Accessibility................................................................................................................1 

 4.4.2 Representative of Average Flow and Water Quality of River Reach.........................2 

 4.4.3 Stable Setting for Long-Term Monitoring..................................................................2 

4.5 Cross-sectional Profile of Flow and Field Water Quality Variables ...................................2 

4.6 Installing a Staff Gage .........................................................................................................3 

4.7 Permanent Markers and Site Coordinates............................................................................3 

4.8 Photographic Documentation...............................................................................................4 

4.9 Creating Field and Office Binders .......................................................................................4 

4.10 Enter Station Information into NPSTORET........................................................................5 

4.11 Quality Assurance/Quality Control Procedures...................................................................5 

4.12 Literature Cited ....................................................................................................................5 

 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #4, page iii 

Revision History Log 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project leader and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log: 

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #4, page iv 

Acknowledgements

The authors would like to acknowledge Susan O’Ney, who blazed the trail when it came to 

writing standard operating procedures for National Park Service water quality monitoring 

protocols. Much of our site establishment SOP is based on her work (O’Ney 2005). Thanks also 

go to Pete Penoyer for his guidance (Penoyer 2003). 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #4, page 1 

4.0 Introduction 

Preliminary site visits are required to formally establish the specific monitoring stations. 

Information on the river cross-section, flow depth, and flow velocity must be gathered, and 

discharge rating curves must be developed. Detailed information on each sampling site must be 

compiled into field binders and must include all material necessary for safe and efficient field 

operations. 

4.1 Establishing NPSTORET Project Files 

Project files should be established prior to site reconnaissance visits using the NPSTORET 

database template. The project manager is responsible for ensuring electronic and paper project 

and site files are established and maintained. NPS policy requires specific information on surface 

water sampling sites. Refer to Tucker (2004) for detailed discussions of NPS data and metadata 

requirements, and to SOP #8 of this protocol for detailed instructions on data entry and 

management. 

4.2 Selection of Proposed Monitoring Stations 

The site selection process and proposed monitoring stations for monitoring water quality in large 

rivers are described in Section 2 of the protocol narrative. The selection process includes 

oversampling of the randomly-selected sites; if any of the proposed monitoring sites that have 

been randomly selected prove to be inappropriate or not representative of the resource being 

monitored, then a replacement must be selected from the pool of oversampled sites. 

4.3 Permission for Research 

Once a proposed station has been identified, permission should be obtained from the appropriate 

park to conduct research and establish permanent markers within park boundaries. Contact the 

park’s research coordinator and complete all required permit application forms prior to 

conducting site establishment activities. 

4.4 Location Reconnaissance and Assessment 

Once a potential monitoring station has been selected and its GPS location verified on a map, the 

site should be visited to assess whether it is an appropriate monitoring location. Water quality 

monitoring sites and flow monitoring sites for a given monitoring station do not need to be at the 

same exact location, but they should be within one mile of each other and represent the same 

flow conditions (no sinks or sources between the two sites). Key concerns are accessibility, 

representativeness, and stability. 

4.4.1 Accessibility 

Bridge crossings provide safe access to large rivers during high flows, but can be the source of 

road contaminants (volatile organic compounds and especially road salts), and rarely cross at 

randomly-selected locations. Therefore it is preferable to sample from boats. Identify the nearest 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #4, page 2 

public access boat landing. The landing should be located within a few miles (<10 miles) of 

proposed monitoring site. Visit the site using the boat that is planned for field work to verify that 

average flow conditions are passable using that boat and the route is not blocked by riffles or 

rapids. Select monitoring locations that allow safe sampling during high flow with minimal risk 

to sampling personnel. 

4.4.2 Representative of Average Flow and Water Quality of River Reach 

At the proposed monitoring location, river discharge should be free-flowing (not stagnant) but 

not overly aerated or churned. The flow conditions should represent well-mixed but laminar 

flow. As part of the reconnaissance, verify that a proposed site is not immediately downstream of 

a pollution point source. If a site has been selected randomly to represent the average conditions 

of the river, then it should be located at least five stream-widths downstream from a tributary to 

ensure complete mixing of waters (Stednick and Gilbert 1998). During reconnaissance of a 

potential site, verify vertical and lateral mixing, as measured by core suite readings of the stream 

cross-section (see section 4.6 below). 

4.4.3 Stable Setting for Long-Term Monitoring 

The proposed monitoring site should be located along a straight portion of the river channel; 

avoid meander bends or side channels that may experience changes in the streambed 

morphology. It is best if the site is entrenched between stable river banks; avoid low banks or 

levees on one or both sides of the river that are prone to overbank flow, unless this is 

representative of the average conditions for this reach. For discharge measurements, it is 

preferable that the selected location is confined between bedrock or high clay banks; avoid sandy 

streambeds. 

4.5 Cross-sectional Profile of Flow and Field Water Quality 

Variables 

Before site establishment can be finalized, mixing must be verified by homogeneous readings of 

the core suite variables (pH, temperature, specific conductivity, and dissolved oxygen) when 

measured in cross-sectional profile. 

To establish a profile of field measurements: 

• Establish a cross-sectional profile of stream discharge. 

• Calculate the proportion of total discharge per unit width of the stream. 

• Determine the increment (vertical) at which discharge in that increment is equal 

(approximately) on both sides of that point; this is the centroid of flow and the point 

at which measurements should be obtained after site establishment. 

• Make individual measurements of required field parameters (temperature, dissolved 

oxygen, pH, and conductivity) at a number of equally spaced verticals along the 

cross-section and at multiple depths within each vertical. 

• Check the cross-sectional profile data to determine the variability of required field 

variables per unit width of the stream. 

• Field measurement profiles of stream variability are needed for low- and high-flow 

conditions and should be verified at least every two years. 

• Record the information collected and include it in the field folders for each station. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #4, page 3 

If the cross-sectional profile of stream discharge and field measurements indicates that the 

section is not homogeneous, repeat the procedure at additional locations until a suitable site has 

been identified. If sampling must be conducted at a highly-desirable site that is poorly mixed, 

then field personnel should follow the instructions for the collection of isokinetic, depthintegrated samples (Webb et al. 1999), which entails collecting multiple samples within the 

cross-section. 

4.6 Installing a Staff Gage 

Each newly established site must be evaluated for the availability of flow data. At some 

monitoring locations where automated USGS flow gages are not located nearby, it may be 

desirable to install a staff gage for the purpose of developing a stage-discharge rating relationship 

or curve. Refer to Magdalene (2008) for an example of rating curve development in a Great 

Lakes Network park. A rating curve is established for a monitoring station by making a series of 

independent flow measurements and simultaneous staff gage measurements at different water 

levels. The stage is plotted versus discharge (typically gage height in feet versus discharge in 

cubic feet per second) on log-log paper. The rating curve converts stage height to discharge, 

enabling calculation of discharge volume from a simple stage height measurement. Discharge 

measurements using the velocity-area method should be made over a range of stage heights. It is 

important that the rating curve include measurements made at flow extremes (i.e., drought and 

flood) to be most accurate. The more points, the more precise the rating curve is likely to be. 

Refer to Rantz (1982) for complete details on the development of rating curves from staff gage 

readings. 

A staff gage is a ruler, usually made of enameled steel, placed in a stream or lake and used to 

measure the water level. Staff gages are usually mounted on permanent structures, such as a 

bridge piling, but may also be sunk into a stable bottom substrate or anchored to bedrock. The 

staff gage should be located in an area that will provide some degree of protection from debris 

flows, etc. The staff gages installed at specific water monitoring locations will be read at the time 

water samples are taken to determine the stage or elevation of the water surface at that location. 

Anchored in the stream bed (or mounted on a bridge), the gage will consist of a vertical scale 

that is permanently marked in increments of 0.01 feet and the stage reads directly from these 

markings to the nearest 0.01 feet. Stream stage is defined as the elevation of the water surface 

above an arbitrary zero datum at that specific point in the stream. Thus, the zero discharge point 

does not necessarily correspond to a stage of zero. The gage may be calibrated by referencing the 

numbered height on the gage to the surveyed elevation of the water surface and its associated 

flow at the time of installation. 

4.7 Permanent Marker and Site Coordinates 

Accurate station location descriptions must be recorded and followed carefully by sampling 

personnel on subsequent field visits. Use Global Positioning System (GPS) equipment to obtain 

the station’s coordinates and elevation near the water’s edge. Read and follow SOP #3 for more 

details on using a GPS unit. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #4, page 4 

After receiving permission from the park, install permanent markers on each river bank to 

delineate a river cross-section at the monitoring site. Record the GPS location of each marker 

and the heading, from right bank to left bank, between markers. On subsequent visits, sampling 

personnel should measure along the same cross-section. 

4.8 Photographic Documentation 

Each sampling site must be documented with a series of photographs to establish site conditions. 

These photographs will be used to accurately relocate monitoring sites and to document field 

conditions. Document initial conditions at the site: take digital photographs of the site from a 

landmark on shore (e.g., boat landing, bridge, campsite), and photographs of the river from the 

site in the upstream and downstream directions. 

Photographs should be identified with: 

• The photograph number 

• Date and time, even if the photographs are automatically date stamped by the camera 

• The subject 

• The location in narrative format and GPS coordinates 

• The photographer 

• Witnesses, if any 

• The location from which the photograph was taken 

• A short narrative description of the photographs 

New photographs should be taken at the beginning of each field season or whenever site 

conditions change substantially. 

4.9 Creating Field and Office Binders 

Selected information that is needed for reference while at a sampling station is kept in a field 

binder. The field binder contains information used by trained personnel to locate and safely 

collect water quality samples and must be taken along on each sampling trip. Assemble and 

update the field binders with information such as description of sampling station, maps, data 

collected at station previously, and sampling instructions. 

The office binder should contain reference information relevant to general field sampling 

procedures with tabs identifying each procedure for easy access during field work, including 

QA/QC reminders, a copy of the protocol narrative and all SOPs, copies of equipment 

instructions and troubleshooting; extra field forms, material safety data sheets for field supplies 

that contain hazardous chemicals or materials, and analytical service request and chain of 

custody forms. 

See SOP #1, Preseason Activities, for more detailed information on preparing field and office 

binders. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #4, page 5 

4.10 Enter Station Information into NPSTORET 

Upon returning to the office, enter all information into NPSTORET following the guidelines for 

establishing a new station record in GLKN’s data management plan (Hart and Gafvert 2005). 

Station IDs should be assigned to new stations based on park unit, river name, and river miles (to 

the nearest 1.0 mile). Prepare a description of the location and compile other required 

information (including digital photographs) for establishing NPSTORET files. 

In addition, information related to the water quality measurements collected at each site must be 

entered into NPSTORET. For a complete list of water quality variables and relevant metatdata 

(i.e., analytical methods), see SOP #7, Processing Water Samples and Analytical Laboratory 

Requirements. Follow details for data entry provided in SOP #8, Data Entry and Management. 

4.11 Quality Assurance/Quality Control

All data entered into NPSTORET should be reviewed for accuracy by the individual entering the 

data. The project manager is responsible for ensuring all QA/QC procedures are followed, 

including proper data entry, validation, and documentation. See SOP #12 for more details on 

QA/QC for data entry and management. 

4.12 Literature Cited 

Hart, M., and U. Gafvert. 2005. Data management plan: Great Lakes Inventory & Monitoring 

Network (draft). National Park Service Great Lakes Inventory and Monitoring Network 

GLKN/2005/20. 

Magdalene, S. 2008. Site establishment for large rivers water quality monitoring: Stage 

discharge relationships at selected sites within the St. Croix National Scenic Riverway. 

National Park Service, Great Lakes Inventory and Monitoring Network Report 

GLKN/2008/02. Available at: http://science.nature.nps.gov/im/units/glkn/index.cfm 

O’Ney, S.E. 2005. Standard operating procedure #1: Initial site establishment, Version 1.0. In: 

Regulatory water quality monitoring protocol, Version 1.0, Appendix E. Bozeman (MT): 

National Park Service, Greater Yellowstone Network. 

Penoyer, P. 2003. Part C: Vital signs longterm aquatic monitoring projects, draft guidance on 

WRD required and other field parameter measurements, general monitoring methods and 

some design considerations in preparation of a detailed study plan, 2003 Aug 6 Draft. in

Guidance on water quality, contaminants, and aquatic biology vital signs monitoring 

under the Natural Resource Challenge Long-Term Water Quality Monitoring Program. 

Fort Collins, Colorado. National Park Service, Water Resources Division. Available 

from: http://science.nature.nps.gov/im/monitor/protocols/wqPartC.doc. 

Rantz, S.E. 1982. Measurement and computation of streamflow, Volume 1: Measurement of 

stage and discharge. Reston (VA): U. S. Geological Survey. Water Supply Paper nr 2175. 

Available from: http://water.usgs.gov/pubs/wsp/wsp2175/. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #4, page 6 

Stednick, J. D., and D. M. Gilbert. 1998. Water quality inventory protocol: riverine 

environments. National Park Service Technical Report NPS/NRWRD/NRTR-98/177. 

http://science.nature.nps.gov/im/monitor/protocols/wrdwq.wpd. 

Tucker, D. 2004. Part E: Draft guidance on data reporting and archiving in STORET. in

Guidance on water quality, contaminants, and aquatic biology vital signs monitoring 

under the Natural Resource Challenge Long-Term Water Quality Monitoring Program. 

Fort Collins, Colorado. National Park Service, Water Resources Division. Available 

from: http://science.nature.nps.gov/im/monitor/protocols/wqPartE.doc

Webb, W. E., D. B. Radtke, and R. T. Iwatsubo. 1999. Collection of water samples: Collection 

methods at flowing-water and still-water sites. in Wilde, F.D., D.B. Radtke, J. Gibs, and 

R.T. Iwatsubo, editors, September 1999, Collection of water samples: U.S. Geological 

Survey Techniques of Water-Resources Investigations, Book 9 (National Field Manual), 

Chapter A4. http://water.usgs.gov/owq/FieldManual/chapter4/html/4.1.1.html.
Standard Operating Procedure #5: Decontamination 

of Equipment to Remove Exotic Species 

Version 1.0 

In Large Rivers Water Quality Monitoring Protocol 

Prepared by 

Joan Elias 

National Park Service 

Great Lakes Inventory and Monitoring Network 

2800 Lake Shore Drive East 

Ashland, Wisconsin 54806 

joan_elias@nps.gov 

August 2008 

Suggested citation: Elias, J. 2008. Standard operating procedure #5: Decontamination of 

equipment to remove exotic species. in Magdalene S., D.R. Engstrom, and J. Elias. 2008. Large 

rivers water quality monitoring protocol, Version 1.0. National Park Service, Great Lakes 

Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/060. National Park Service, Fort 

Collins, Colorado.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page ii

Contents 

 Page

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

5.0 Introduction..........................................................................................................................1 

5.1 Equipment and Supplies ......................................................................................................1 

5.2 Decontamination Procedures ...............................................................................................2

 5.2.1 Aquatic Invasive Species Procedure Plan and Hazard Analysis Worksheet ..............2 

 5.2.2 Step-by-Step Procedures for Decontamination...........................................................2 

 5.2.3 Park-Specific Requirements........................................................................................3 

5.3 Documentation.....................................................................................................................3 

5.4 Literature Cited ....................................................................................................................3 

Appendix A. Instructions for completing a hazard analysis and critical control point plan............5 

Appendix B. An example of a plan for the control of aquatic invasive species at Mississippi 

National River and Recreation Area................................................................................................9 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page iii

Revision History Log 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project manager must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the header of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log: 

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page iv

Acknowledgements 

I wish to thank Jeff Gunderson and Doug Jensen, of the Minnesota Sea Grant Program, Phil 

Moy, of the Wisconsin Sea Grant Program, and Mike Klepinger, of the Michigan Sea Grant 

Program for their willingness to discuss exotic species issues in national parks and for providing 

information on the Hazard Analysis Critical Control Point (HACCP) method. Thanks especially 

to Phil Moy for reviewing an earlier draft of this document. Jennifer Sieracki, National Park 

Service - Great Lakes Inventory and Monitoring Network prepared the HACCP plan (Appendix 

B).
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 1

5.0 Introduction

Aquatic invasive species (AIS) are an issue of increasing concern nationwide. In the Great 

Lakes, for example, approximately 140 exotic species have invaded since the late 1800s (Great 

Lakes Information Network 2005) and have had enormous ecosystem effects (e.g., Dermott and 

Kerec 1997; Barnhisel and Kerfoot 2004; Hoff 2004; Great Lakes Commission 2005). Some of 

these species have invaded inland water bodies, where disruptions to native species are also 

documented (e.g., Jack and Thorp 2000; Indrisi et al. 2001; Compton and Kerfoot 2004). Zebra 

mussels (Dreissena polymorpha) now occur in several lakes at Sleeping Bear Dunes National 

Lakeshore, and the spiny waterflea (Bythotrephes cederstroemi) has been found in lakes at both 

Pictured Rocks National Lakeshore and Voyageurs National Park. When the parks and Great 

Lakes Network conduct routine water quality monitoring, it is important to ensure these aquatic 

exotics are not transferred from contaminated water bodies to uncontaminated water bodies. 

As we implement our water quality monitoring program, we are concerned with the limited suite 

of AIS that can adhere to, or passively catch on, sampling equipment (including boats and 

trailers). In this standard operating procedure (SOP) we will focus on aquatic plants, 

zooplankton, and mussels. 

At each park, we will use the Hazard Analysis Critical Control Point (HACCP) method 

(Gunderson and Kinuunen 2004) to identify water bodies at risk and locations where control of 

AIS is imperative. It is critical to integrate this SOP with monitoring for the occurrence of AIS in 

park lakes and rivers. 

5.1 Equipment and Supplies

The sampling equipment used in routine water quality monitoring is detailed in SOP #6. Of 

particular importance in this decontamination SOP, is that nets are not currently used in routine 

water quality monitoring. If nets are added to the equipment used in any part of water quality 

monitoring, this decontamination SOP should be modified to include specific decontamination 

procedures for nets. 

The supplies and equipment required for decontamination of sampling equipment between lakes 

consists of: 

o tap water 

o hose and sprayer nozzle 

o portable containers for lake water, such as a bucket or cubitainer 

o scrub brush 

o bottle brush on a rope 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 2

5.2 Decontamination Procedures 

5.2.1 Aquatic Invasive Species Procedure Plan and Hazard Analysis Worksheet 

The aquatic invasive species hazard analysis and critical control point (HACCP) worksheet is 

used in describing the sampling project, including types of gear, methods of transportation, steps 

involved in the procedure; and analyzing the potential risk of AIS transport from one water body 

to another, or one section of a river to another section. The example included here, in Appendix 

A, is for Mississippi National River and Recreation Area. Details on completing the worksheet 

are described in the AIS-HACCP manual (Gunderson and Kinuunen 2004), and are included in 

Appendix B. The Network has modified the worksheet slightly to suit our needs. Worksheets 

will be completed for each park unit, and will be updated annually prior to the sampling season. 

Worksheets will also be updated in the following circumstances: 

• change in sampling equipment or techniques 

• Addition of a new water body or river site to the sampling regime 

• Change in the order of sampling water bodies 

• Detection of a new AIS in a water body or section of river 

• Change in scientific knowledge regarding life history, potential hazard, or control of an 

AIS 

5.2.2 Step-by-Step Procedures for Decontamination 

When the hazard analysis worksheet identifies a significant AIS risk and adequate drying or 

freezing of equipment is not feasible (five days in the sun for boats and trailers, 10 days for other 

equipment, or two days of freezing; Gunderson and Kinuunen 2004), one of the two procedures 

below, for remote locations or locations where tap water is available, will be followed. 

Procedure at remote locations

When finished at a segment of river that is known or suspected to be infested with exotic species: 

• Remove and rinse mud, plant material, mussels, and other visible organic material from 

boat/canoe, paddles/oars, boots, and all sampling equipment 

• Run hand up and down ropes attached to all equipment and anchor to dislodge mud, plant 

material, and organisms 

• Pay particular attention to cracks and crevices in equipment when rinsing 

• Visually inspect all gear to verify that all equipment and gear has been cleaned and rinsed 

Before entering a new segment of the river that is not known to contain exotic species: 

• Use a clean and dry container, such as cubitainer or bucket to collect river water 

• on vegetated land away from the bank of the river, rinse and scrub with (clean) scrubbrush all sampling equipment, boat/canoe, paddles/oars, boots, etc. Avoid rinsing on 

impervious surfaces or slopes where rinse water might run directly into the river 

• Use a bottle brush on a rope to clean the inside of the integrated sampler 

• Pay particular attention to ropes, cracks, and crevices in equipment, and rinse well 

• Visually inspect all gear to verify that all equipment and gear has been cleaned and rinsed 

Procedure at non-remote locations, when tap water is available

When finished at a segment of river that is known or suspected to be infested with exotic species: 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 3

• remove or rinse mud, plant material, mussels, and other visible organic material from 

boat/canoe, paddles/oars, boots, and all sampling equipment. 

Before entering a new segment of the river that is not known to contain exotic species: 

• on vegetated land, use hose with spray nozzle and scrub brush to rinse and scrub with tap 

water and scrub-brush all sampling equipment, boat/canoe, paddles/oars, boots; discard 

water on land, away from the bank of the river, avoiding impervious surfaces and slopes 

where rinse water might run directly into the river; 

• use a bottle brush on a rope to clean the inside of the integrated sampler; 

• pay particular attention to ropes, cracks, and crevices in equipment, and rinse well; 

• visually inspect all gear to verify that all equipment and gear has been cleaned and rinsed. 

Regardless of remoteness

• When possible, avoid using boats and other equipment on both infested and uninfested 

waters. Designate a set of equipment for both types of waters. 

• Always begin sampling with lakes not known to harbor exotic species; sample lakes 

known or suspected to contain exotic species last. 

• Thoroughly clean or disinfect all equipment between use in infested and uninfested 

waters. 

• When possible, allow boat/canoe and paddles/oars to dry for five days and all other 

sampling equipment boots to dry for 10 days after sampling a water body known to be 

infested with AIS. 

5.2.3 Park-Specific Requirements 

Some parks may have specific requirements for decontamination of equipment. For example, 

both Voyageurs and Isle Royale National Parks require that equipment and gear used in water 

quality sampling be treated in hot water (60°C [140 °F], for >2 min.). The Network will always 

adhere to park requirements. 

5.3 Documentation 

The original AIS-HACCP worksheet and all updates will be maintained at each park and copies 

will be kept at the Network office. Documents used to complete each worksheet will also be kept 

on file at the parks and at the Network. Examples of such supporting documentation include 

information used in analyzing the hazards of contamination and determining adequate prevention 

of AIS spread, and the most current geographic range of AIS. When the water quality monitoring 

protocol is integrated with monitoring for AIS, the AIS monitoring report will also be kept at 

each park and at the Network office. 

5.4 Literature Cited 

Barnhisel, D. R., and C. Kerfoot. 2004. Fitting into food webs: Behavioral and functional 

response of young lake trout (Salvelinus namaycush) to an introduced prey, the spiny 

cladoceran (Bythotrephes cederstroemi). Journal of Great Lakes Research 30:300-314. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 4

Compton, J. A. ,and C. Kerfoot. 2004. Colonizing inland lakes: Consequences of YOY fish 

ingesting the spiny cladoceran (Bythotrephes cederstroemi). Journal of Great Lakes 

Research 30:315-326. 

Dermott, R., and D. Kerec. 1997. Changes to the deepwater benthos of eastern Lake Erie since 

the invasions of Dreissena: 1979-1993. Canadian Journal of Fisheries and Aquatic 

Science 54:922-930. 

Gunderson, J. L., and R. Kinnunen. 2004. AIS-HACCP: Aquatic nuisance species – hazard 

analysis and critical control point training curriculum. Second edition. Minnesota Sea 

Grant Publ. MN SG-F11. 

Great Lakes Information Network. 2005. http://www.great-lakes.net/envt/florafauna/invasive/invasive.html. Accessed June 7, 2005. 

Great Lakes Commission. 2005. Great Lakes Panel on Aquatic Nuisance Species. 

Counterattack: Great Lakes Panel Targets Aquatic Nuisance Species. 

http://www.glc.org/ans/counterattack.html. Accessed June 7, 2005.

Hoff, M. H. 2004. Biotic and abiotic factors related to rainbow smelt recruitment in the 

Wisconsin waters of Lake Superior, 1978–1997. Journal of Great Lakes Research 

30:414-422. 

Indrisi, N., E. L. Mills, L. G. Rudstam, and D. J. Stewart. 2001. Impact of zebra mussels 

(Dreissena polymorpha) on the pelagic lower trophic levels of Oneida Lake, New York. 

Canadian Journal of Fisheries and Aquatic Science 58:1430-1441. 

Jack, J. D., and J. H. Thorp. 2000. Effects of the benthic suspension feeder Dreissena

polymorpha on zooplankton in a large river. Freshwater Biology 44:569-580. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 5

Appendix A. Instructions for Completing a Hazard Analysis 

and Critical Control Point Plan

The following instructions for completing HACCP Procedure Form, Potential Hazards 

Worksheet, Hazard Analysis Worksheet, and Plan are taken directly from the AIS-HACCP 

manual (Gunderson and Kinuunen 2004). Not all steps will apply to the Great Lakes Inventory 

and Monitoring Network’s protocol for decontamination of water quality monitoring field 

equipment and gear. 

Preliminary Steps 

1: Document general information. 

Record the name and address of your facility or agency in the spaces provided on the first page 

of the Hazard Analysis Worksheet and the AISHACCP Plan Form (Appendix 9). 

2: Describe the cultured or wild harvested fish (if applicable). 

Identify the market name or Latin name (species) of the fish. 

examples: 

o Fathead minnows (Pimephales promelas) 

o Golden shiners (Notemigonus crysoleucas) 

o White sucker (Catostomus commersoni) 

o Walleye (Sander vitreus) 

Fully describe the product. 

examples: 

o Fathead minnows graded on 16 grader 

o Golden shiners graded on 21 grader 

o White suckers ungraded 

o Rosy red minnows from Arkansas, held in ponds until distribution 

o White suckers graded on a 23 grader 

o Walleye fingerlings 5 - 8 inches 

o Yellow perch fingerlings 2.5 - 3 inches 

For management, research, and enforcement activities: 

o Completely describe research or management activities 

o Describe all equipment and gear that will be used 

o Identify when and how activities will be conducted 

Record this information in the spaces provided on the first page of the Hazard Analysis 

Worksheet and the AIS-HACCP Plan Form. 

3: Describe the harvest, production, management, research, or enforcement activity. 

Identify how the product or the samples are collected, stored, and distributed. Identify whether 

any special shipping or handling methods are used. 

examples: 

o Wild harvested with seines, held in tanks, graded, then trucked to retail stores 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 6

o Pond-raised, seined, then held in different ponds over the winter, trucked to retail stores 

o Pond-raised, trapped from ponds, then transferred directly to lakes for stocking 

o Anglers on three lakes are checked for violations each day for a given period of time 

o Electroshocking and seining are conducted on 10 lakes to assess year class strength 

Record this information in the spaces provided on the first page of the Hazard Analysis 

Worksheet and the AIS-HACCP Plan Form. 

 

4: Identify the intended use and customer (if applicable). 

Identify how the product will be used. 

examples: 

o Live fishing bait 

o Feeder fish (feeding pond or aquarium fish) 

o Stocking into public waters 

o Stocking into private waters 

o Stocking into aquaculture production facility (indoor or outdoor) 

o Scale and stomach samples will be brought back to the office for analysis 

o Fish will be brought back for captive brood stock 

Identify your intended customer or user of the product. 

examples: 

o General public 

o A wholesaler 

o A retail store 

o Fish farmer 

o State agency 

Record this information in the spaces provided on the first page of the Hazard Analysis 

Worksheet and the AIS-HACCP Plan Form. 

5: Develop a flow diagram. 

The purpose of the flow diagram is to provide a clear, simple description of the steps involved in 

producing your fishery products or conducting your management, research, and enforcement 

activities. The flow diagram should cover all of the steps in the process that your firm or agency 

performs. The flow diagram should be verified on-site for accuracy. Examples of flow diagrams 

can be found in appendices 3-8. 

Hazard Analysis Worksheet 

6: Set up the Hazard Analysis Worksheet. 

Record each of the steps from the flow diagram in column 1 of the Hazard Analysis Worksheet. 

7: Identify the potential AIS-related hazards. 

Record the AIS-related hazards for each step. Use your own expertise and that of others to 

identify AIS hazards related to your fish production, or management, research, or enforcement 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 7

practices. Check with appropriate agencies to determine if the waters in which you conduct 

activities are infested with invasive species. 

Even if you think you have effective hazard controls in place, record the hazard. For example, 

your equipment might be free of AIS plant material because of the: 1) absence of AIS in the area 

of harvest or sampling in an infested water body; or 2) existence of inadvertent hazard controls 

(procedures you typically use in the course of your activities that may remove AIS). 

8: Complete the Hazard Analysis Worksheet. 

Completing the Hazard Analysis Worksheet requires understanding potential hazards, 

determining if each potential hazard is significant, and identifying critical control points for each 

significant hazard associated with your product or activities. 

AIS –HACCP Plan Form 

9: Complete the AIS-HACCP Plan Form. 

Copy the Critical Control Points from column 6 of the Hazard Analysis Worksheet to column 1 

of the AIS-HACCP Plan Form. Enter the associated hazard(s) from column 2 of the worksheet to 

column 2 of the plan form. If you did not identify significant hazards and CCPs, you do not need 

to complete an AIS-HACCP plan. 

Complete the AIS-HACCP Plan Form by designing techniques, methods, and treatments to deal 

with each significant hazard in column 2. For each significant hazard: 

o set critical limits 

o establish monitoring procedures 

o establish corrective action procedures 

o establish a record keeping system 

o establish verification procedures 

After you completed these steps for each hazard, the AIS-HACCP plan form is finished. 

To signify that the AIS-HACCP plan has been accepted for implementation, the responsible 

individual on-site or a higher level official should sign and date the first page of the plan form. 

Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 9

Appendix B. An Example of a Plan for Control of Aquatic 

Invasive Species at Mississippi National River and 

Recreation Area. 

 

Aquatic Invasive Species - Hazard Analysis and Critical 

Control Point Procedure Form 

 

Procedure Description 

Park info: Park name: Mississippi National River and Recreation Area

 

 

Address: 111 Kellogg Blvd E, Ste 105

City: St. Paul State: MN Zip: 55101

(if applicable): 

 Fish species: NA

Management, research, 

or monitoring activity: Activity: Water Quality Monitoring

 

Method of transportation, 

distribution, and 

storage of boats, gear, etc. 

 

Methods: Boat and gear either trailered or portaged to public landing sites. 

Profiles of water temperature, dissolved oxygen, specific conductance, and 

pH are conducted with multi-probe sonde. Water is collected with an 

integrated sampler for lab analyses. Multiple locations on the river will be 

sampled in one day.

(1) Day 1: NPS staff drive to boat access in Dayton, boat 1/3 mi upstream (RM880), conduct 

WQ monitoring with sonde, and collect water samples with integrated sampler for lab 

analyses. Return to truck.

List the steps involved in the 

management, research, or 

monitoring activity. 

(2) Day 1 continued: Drive downstream to River Park. Put in, travel 1.10 mi downstream 

(RM862), conduct WQ monitoring, and collect water samples. Return boat to truck.

(3) Day 1 continued: Drive downstream to 8th Ave NE bridge. Launch boat from Boom 

Island, travel 1/4 mi. upstream (RM855). Return boat to truck.

(4) Day 2: Drive to canoe landing in small park on east bank just south of UM campus. 

Canoe 1/3 mi downstream (RM852). Conduct WQ monitoring and collect water samples. 

Return canoe to car.

Include a simple, but, complete, 

description of the procedure. 

List all steps within NPS control, 

but only as many steps as 

necessary to define the 

procedure. 

(5) Day 2 continued: Drive downstream to Bud's Landing. Launch boat from public access, 

travel upstream 1 mi (RM822), conduct WQ monitoring, and collect water samples. Return 

boat to car and back to SACN.

 

 

(6) At the end of sampling, water samples are processed back at the lab at SACN.

 

 

(7) 

 

 

(8) 

 

 

(9) 

 

 

(10) 

Next Step: 

Complete the potential 

(11) 

hazards worksheet. 

 (12) 

 

Upon completion of the 

AIS-HACCP plan, sign 

Name: 

here to accept plan for 

implementation Signature: Date: 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 10

AIS-HACCP PLAN 

Aquatic Invasive Species - Hazard Analysis and Critical Control Point 

Potential Hazards 

Worksheet 

 

Potential AIS Hazards 

 

List all relevant species 

 

Examples: round goby, 

ruffe, carp, etc. 

 AIS Fish and Other Vertebrates 

N/A 

 

Examples: zebra mussel, 

spiny waterflea, rusty 

crayfish, etc. 

 

 

 

 

 

 

 AIS Invertebrates 

St. Anthony Falls downstream beyond the park border is declared infested by zebra 

mussels (Dreissena polymorpha) by the MNDNR. 

Rusty crayfish (Orconectes rusticus) has not been found to infest the river, but may 

still exist in it. This species typically does not stowaway on boats, but should be 

checked for regardless. 

Examples: curly 

pondweed, 

Eurasian water-milfoil, 

etc. 

 

 

 

 

 AIS Plants 

St. Anthony Falls downstream beyond the park border is declared infested by 

Eurasian watermilfoil (Myriophyllum spicatum) by the MNDNR. 

 

Examples: whirling 

disease, hotspots, etc. 

 

 

Next Step: 

After identifying the 

potential hazards, 

complete a hazard 

a hazard analysis form. 

 AIS Pathogens 

N/A 

 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 11

AIS-HACCP 

PLAN 

Aquatic Invasive Species - Hazard Analysis and Critical Control Point 

Hazard Analysis 

Worksheet 

(1) Activity (2) Hazards (3) (4) Justification (5) Control (6) CCP 

Activity step from flow 

diagram, page 1 

Potential AIS 

hazards introduced 

or controlled at this 

step (from potential 

hazards worksheet) 

Are AIS 

hazards 

significant 

(Yes/No) 

Justify your decisions 

for column 3. 

What control 

measures will be 

applied to prevent 

the significant 

hazards? 

Is this step 

a critical 

control 

point? 

(Yes/No) 

 

Fish/Other 

Vertebrates 

N/A No 

Boat and equipment 

used will not capture 

any fish. 

 No 

Invertebrate 

Zebra Mussels 

Rusty Crayfish Unknown 

Possibility of rusty 

crayfish, though not 

verified 

Zebra mussels 

expected 2006 

Inspect boat for 

possible stowaway 

crayfish; travel 

downstream to 

prevent introducing 

zebra mussels 

Yes 

Plant 

None

No 

No plant AIS occur 

upstream of St. 

Anthony Falls 

 No 

Work Flow Step (1) 

Day 1: NPS staff drive to 

boat access in Dayton, boat 

1/3 mi upstream (RM880), 

conduct WQ monitoring with 

sonde, and collect water 

samples with integrated 

sampler for lab analyses. 

Return to truck.

Pathogens 

N/A

No AIS pathogens not 

present. No 

 

Fish/Other 

Vertebrates 

N/A No 

Boat and equipment 

used will not capture 

any fish 

 No 

Invertebrate 

Zebra Mussels 

Rusty Crayfish Unknown 

Possibility of rusty 

crayfish, though not 

verified 

Zebra mussels 

expected 2006 

Inspect boat for 

possible stowaway 

crayfish; travel 

downstream to 

prevent introducing 

zebra mussels 

Yes 

Plant 

None

No 

No plant AIS occur 

upstream of St. 

Anthony Falls 

 No 

Work Flow Step (2) 

Day 1 continued: Drive 

downstream to River Park. 

Put in, travel 1.10 mi 

downstream (RM862), 

conduct WQ monitoring and 

collect water samples. 

Return boat to truck.

Pathogens 

N/A

No AIS pathogens not 

present. No 

Next Step: Once you have determined the critical control points of your procedure, enter them in row 1 of the HACCP plan 

form. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 12

AIS-HACCP 

PLAN 

Aquatic Invasive Species - Hazard Analysis and Critical Control Point 

Hazard Analysis 

Worksheet 

 

(1) Activity (2) Hazards (3) (4) Justification (5) Control (6) CCP 

Activity step from flow 

diagram, page 1 

Potential AIS hazards 

introduced or controlled 

at this step (from 

potential hazards 

worksheet) 

Are AIS 

hazards 

significant 

(Yes/No) 

Justify your decisions 

for column 3. 

What control 

measures will be 

applied to prevent 

the significant 

hazards? 

Is this step 

a critical 

control 

point? 

(Yes/No) 

Fish/Other Vertebrates 

N/A

No 

Boat and equipment 

used will not capture 

any fish 

 No 

Invertebrate 

Zebra Mussels 

Rusty Crayfish Unknown 

Possibility of rusty 

crayfish, though not 

verified 

Zebra mussels 

expected 2006 

Inspect boat for 

possible stowaway 

crayfish; travel 

downstream to 

prevent introducing 

zebra mussels 

Yes 

Plant 

None

No 

No plant AIS occur 

upstream of St. 

Anthony Falls 

 No 

Work Flow Step (3) 

Day 1 continued: Drive 

downstream to 8th Ave 

NE bridge. Sample from 

bridge if traffic allows for 

it. Otherwise, launch 

boat from Boom Island, 

travel 1/4 mi. upstream 

(RM855). Return boat to 

truck.

Pathogens 

N/A

No AIS pathogens not 

present. No 

 

Fish/Other Vertebrates 

N/A

No 

Boat and equipment 

used will not capture 

any fish 

 No 

Invertebrate 

Zebra Mussels 

Rusty Crayfish Yes 

Zebra mussel infested 

location 

Possibility of rusty 

crayfish though not 

verified 

If traveling to noninfested area, boat 

and equipment 

should be sprayed 

with hot water 

(140F) 

Yes 

Plant 

Eurasian Watermilfoil

Yes Eurasian watermilfoil 

infested location 

Inspect boat, rope, 

and anchor after 

sampling; remove 

any mud and plant 

material 

Yes 

Work Flow Step (4) 

Day 2: Drive to canoe 

landing in small park on 

east bank just south of 

UM campus. Canoe 1/3 

mi downstream 

(RM852). Conduct WQ 

monitoring and collect 

water samples. Return 

canoe to car.

Pathogens 

N/A

No AIS pathogens not 

present. No 

 

Next Step: 

Once you have determined the critical control points of your procedure, enter them in row 1 of the HACCP plan form. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 13

AIS-HACCP 

PLAN 

Aquatic Invasive Species - Hazard Analysis and Critical Control Point 

Hazard Analysis 

Worksheet 

 

(1) Activity (2) Hazards (3) (4) Justification (5) Control (6) CCP 

Activity step from flow 

diagram, page 1 

Potential AIS hazards 

introduced or controlled 

at this step (from 

potential hazards 

worksheet) 

Are AIS 

hazards 

significant 

(Yes/No) 

Justify your decisions 

for column 3. 

What control 

measures will be 

applied to prevent 

the significant 

hazards? 

Is this step 

a critical 

control 

point? 

(Yes/No) 

Fish/Other Vertebrates 

N/A No 

Boat and equipment 

used will not capture 

any fish 

 No 

Invertebrate 

Zebra Mussels 

Rusty Crayfish Yes 

Zebra mussel infested 

location 

Possibility of rusty 

crayfish though not 

verified 

If traveling to noninfested area, 

boat and 

equipment should 

be sprayed with 

hot water (140F) 

Yes 

Plant 

Eurasian Watermilfoil Yes Eurasian watermilfoil 

infested location 

Inspect boat, 

rope, and anchor 

after sampling; 

remove any mud 

and plant material 

Yes 

Work Flow Step (5) 

Day 2 continued: Drive 

downstream to Bud's 

Landing. Launch boat 

from public access, 

travel upstream 1 mi 

(RM822), conduct WQ 

monitoring, and collect 

water samples. Return 

boat to car and back to 

SACN.

Pathogens 

N/A No AIS pathogens not 

present. No 

 

Fish/Other Vertebrates 

N/A No 

Boat and equipment 

used will not capture 

any fish 

 No 

Invertebrate 

Zebra Mussels 

Rusty Crayfish Yes 

It is possible for 

sampling equipment to 

contain zebra mussel 

veligers after exposure 

to infested areas 

All equipment 

should be rinsed 

with hot water 

(140F) or allowed 

to dry completely 

for 5 days 

Yes 

Plant 

Eurasian Watermilfoil No 

Processing equipment 

used will not transfer 

plant AIS 

 No 

Work Flow Step (6) 

At the end of sampling, 

water samples are 

processed back at the 

lab at SACN.

Pathogens 

N/A No AIS pathogens not 

present. No 

(add additional pages as needed) 

Next Step: Once you have determined the critical control points of your procedure, enter them in row 1 of the HACCP plan 

form. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 14

AIS-HACCP PLAN 

Aquatic Invasive Species - Hazard Analysis and Critical Control Point AIS-HACCP Plan Form 

 

Critical 

Control Point 

Each row answered "yes" 

in column 6 of Hazard 

Analysis Form 

 

(1) Day 1: NPS staff drive to boat 

access in Dayton, boat 1/3 mi upstream 

(RM880), conduct WQ monitoring with 

sonde, and collect water samples with 

integrated sampler for lab analyses. 

Return to truck.

Day 1 continued: Drive downstream to River 

Park. Put in, travel 1.10 mi downstream 

(RM862), conduct WQ monitoring and collect 

water samples. Return boat to truck. 

Significant 

Hazards 

as determined in column 3 

of Hazard Analysis Form 

(2) There is a possibility that rusty 

crayfish may exist, but this has never 

been verified. Zebra mussels currently 

do not exist between Brainerd and St. 

Anthony Falls, but are expected to arrive 

in the area this year.

There is a possibility that rusty crayfish may 

exist, but this has never been verified. Zebra 

mussels currently do not exist between Brainerd 

and St. Anthony Falls, but are expected to arrive 

in the area this year. 

Limits for Each 

Control Measure 

 

(3) No rusty crayfish or zebra mussels 

(adults and veligers) remain on boating 

equipment prior to entering non-infested 

waters. Monitoring will be conducted in a 

downstream direction towards increased 

infestation.

No rusty crayfish or zebra mussels (adults and 

veligers) remain on boating equipment prior to 

entering non-infested waters. Monitoring will be 

conducted in a downstream direction towards 

increased infestation. 

Monitoring 

Describe what is being 

monitored 

 

(4) Presence of exotic invertebrates. 

Ensure boat and all equipment are free 

of zebra mussels and rusty crayfish. 

Presence of exotic invertebrates. Ensure boat 

and all equipment are free of zebra mussels and 

rusty crayfish. 

Explain how the monitoring 

will take place 

 

(5) Visual inspection for rusty crayfish 

and zebra mussels. 

Visual inspection for rusty crayfish and zebra 

mussels. 

Frequency of monitoring 

 

(6) Each time, before and after 

equipment is used at RM880. 

Each time, before and after equipment is used 

RM862. 

Person or position 

responsible for monitoring 

(7) Water quality monitoring staff. Water quality monitoring staff. 

Corrective Actions 

Actions taken when limits 

of control measures are 

not met 

(8) Cease operation and remove all 

rusty crayfish. Clean the boat and 

equipment with hot water (140F) or allow 

to dry completely for 5 days prior to 

entering non-zebra mussel infested 

waters.

Cease operation and remove all rusty crayfish. 

Clean the boat and equipment with hot water 

(140F) or allow to dry completely for 5 days prior 

to entering non-zebra mussel infested waters. 

Verification 

Method of verification 

 

(9) Review records. Review records. 

Records 

List what is recorded at 

each critical control point 

 

(10) Record the procedure used to 

remove rusty crayfish or zebra mussels. 

Record that inspections occurred prior to 

leaving one site and before entering the 

next.

Record the procedure used to remove rusty 

crayfish or zebra mussels. Record that 

inspections occurred prior to leaving one site and 

before entering the next. 

 

This form accommodates 2 Critical Control points. Attach additional pages of this form as necessary. 

 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 15

AIS-HACCP PLAN 

Aquatic Invasive Species - Hazard Analysis and Critical Control Point AIS-HACCP Plan Form 

 

Critical 

Control Point 

Each row answered "yes" 

in column 6 of Hazard 

Analysis Form 

 

(1) Day 1 continued: Drive downstream 

to 8th Ave NE bridge. Sample from 

bridge if traffic allows for it. Otherwise, 

launch boat from Boom Island, travel 1/4 

mi. upstream (RM855). Return boat to 

truck. 

Day 2: Drive to canoe landing in small park on 

east bank just south of UM campus. Canoe 1/3 

mi downstream (RM852). Conduct WQ 

monitoring and collect water samples. Return 

canoe to car. 

Significant 

Hazards 

as determined in column 3 

of Hazard Analysis Form 

(2) There is a possibility that rusty 

crayfish may exist, but this has never 

been verified. Zebra mussels currently 

do not exist between Brainerd and St. 

Anthony Falls, but are expected to arrive 

in the area this year.

This area has been designated as zebra mussel 

infested by the MNDNR. There is also a 

possibility that rusty crayfish may exist, but this 

has never been verified. 

Limits for Each 

Control Measure 

 

(3) No rusty crayfish or zebra mussels 

(adults and veligers) remain on boating 

equipment prior to entering non-infested 

waters. Monitoring will be conducted in a 

downstream direction towards increased 

infestation.

No zebra mussels (adults and veligers) or rusty 

crayfish remain on boating equipment prior to 

entering non-infested waters. Monitoring will be 

conducted in a downstream direction towards 

increased infestation. 

Monitoring 

Describe what is being 

monitored 

 

(4) Presence of exotic invertebrates. 

Ensure boat and all equipment are free 

of zebra mussels and rusty crayfish. 

Presence of exotic invertebrates. Ensure boat 

and all equipment are free of zebra mussels and 

rusty crayfish. 

Explain how the monitoring 

will take place 

 

(5) Visual inspection for rusty crayfish 

and zebra mussels. 

Visual inspection for zebra mussels and rusty 

crayfish. 

Frequency of monitoring 

 

(6) Each time, before and after 

equipment is used at RM855.

Each time, before and after equipment is used at 

RM852. 

Person or position 

responsible for monitoring 

(7) Water quality monitoring staff. Water quality monitoring staff. 

Corrective Actions 

Actions taken when limits 

of control measures are 

not met 

(8) Cease operation and remove all 

rusty crayfish. Clean the boat and 

equipment with hot water (140F) or allow 

to dry completely for 5 days prior to 

entering non-zebra mussel infested 

waters.

Cease operation and remove all rusty crayfish. 

Clean the boat and equipment with hot water 

(140F) or allow to dry completely for 5 days prior 

to entering non-zebra mussel infested waters. 

Verification 

Method of verification 

 

(9) Review records. Review records. 

Records 

List what is recorded at 

each critical control point 

 

(10) Record the procedure used to 

remove rusty crayfish or zebra mussels. 

Record that inspections occurred prior to 

leaving one site and before entering the 

next.

Record the procedure used to remove zebra 

mussels and rusty crayfish. Record that 

inspections occurred prior to leaving one site and 

before entering the next. 

 

This form accommodates 2 Critical Control points. Attach additional pages of this form as necessary. 

 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 16

AIS-HACCP PLAN 

Aquatic Invasive Species - Hazard Analysis and Critical Control Point AIS-HACCP Plan Form 

 

Critical 

Control Point 

Each row answered "yes" 

in column 6 of Hazard 

Analysis Form 

 

(1) Day 2: Drive to canoe landing in 

small park on east bank just south of UM 

campus. Canoe 1/3 mi downstream 

(RM852). Conduct WQ monitoring and 

collect water samples. Return canoe to 

car.

Day 2 continued: Drive downstream to Bud's 

Landing. Launch boat from public access, travel 

upstream 1 mi (RM822), conduct WQ 

monitoring, and collect water samples. Return 

boat to car and back to SACN. 

Significant 

Hazards 

as determined in column 3 

of Hazard Analysis Form 

(2) This area has been designated as 

infested by Eurasian watermilfoil by the 

MNDNR.

This area has been designated as zebra mussel 

infested by the MNDNR. There is also a 

possibility that rusty crayfish may exist, but this 

has never been verified. 

Limits for Each 

Control Measure 

 

(3) No viable plant parts remain on the 

boat or equipment.

No zebra mussels (adults and veligers) or rusty 

crayfish remain on boating equipment prior to 

entering non-infested waters. Monitoring will be 

conducted in a downstream direction towards 

increased infestation. 

Monitoring 

Describe what is being 

monitored 

 

(4) Presence of exotic plant material. 

Ensure that boat and all equipment is 

free of viable plant parts.

Presence of exotic invertebrates. Ensure boat 

and all equipment are free of zebra mussels and 

rusty crayfish. 

Explain how the monitoring 

will take place 

 

(5) Visual inspection of boat and other 

equipment for plant fragments.

Visual inspection for zebra mussels and rusty 

crayfish. 

Frequency of monitoring 

 

(6) Each time, before and after 

equipment is used at RM852.

Each time, before and after equipment is used at 

RM822. 

Person or position 

responsible for monitoring 

(7) Water quality monitoring staff. Water quality monitoring staff. 

Corrective Actions 

Actions taken when limits 

of control measures are 

not met 

(8) Cease operation and clean 

equipment before launching onto water.

Cease operation and remove all rusty crayfish. 

Clean the boat and equipment with hot water 

(140F) or allow to dry completely for 5 days prior 

to entering non-zebra mussel infested waters. 

Verification 

Method of verification 

 

(9) Review records. Review records. 

Records 

List what is recorded at 

each critical control point 

 

(10) Record the procedure used to 

remove plant fragments. Record that 

inspections occurred prior to leaving one 

site and entering the next.

Record the procedure used to remove zebra 

mussels and rusty crayfish. Record that 

inspections occurred prior to leaving one site and 

before entering the next. 

 

This form accommodates 2 Critical Control points. Attach additional pages of this form as necessary. 

 

 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 17

AIS-HACCP PLAN 

Aquatic Invasive Species - Hazard Analysis and Critical Control Point AIS-HACCP Plan Form 

 

Critical 

Control Point 

Each row answered "yes" 

in column 6 of Hazard 

Analysis Form 

 

(1) Day 2 continued: Drive downstream 

to Bud's Landing. Launch boat from 

public access, travel upstream 1 mi 

(RM822), conduct WQ monitoring, and 

collect water samples. Return boat to car 

and back to SACN.

At the end of sampling, water samples are 

processed back at the lab at SACN. 

Significant 

Hazards 

as determined in column 3 

of Hazard Analysis Form 

(2) This area has been designated as 

infested by Eurasian watermilfoil by the 

MNDNR.

It is likely that zebra mussel veligers will remain 

on the boat and equipment after being removed 

from infested waters and returned to the lab. 

Limits for Each 

Control Measure 

 

(3) No viable plant parts remain on the 

boat or equipment.

No viable zebra mussels (including veligers) 

remain on the boat and equipment. 

Monitoring 

Describe what is being 

monitored 

 

(4) Presence of exotic plant material. 

Ensure that boat and all equipment is 

free of viable plant parts.

Presence of zebra mussel adults and veligers. 

Ensure that all equipment is free from zebra 

mussels. 

Explain how the monitoring 

will take place 

 

(5) Visual inspection of boat and other 

equipment for plant fragments.

Visual inspection of equipment for adult zebra 

mussels. Veligers can only be seen 

microscopically, but should be assumed to be 

present. 

Frequency of monitoring 

 

(6) Each time, before and after 

equipment is used at RM822.

After equipment has been used in infested 

waters and prior to it being used in non-infested 

waters. 

Person or position 

responsible for monitoring 

(7) Water quality monitoring staff. Water quality monitoring staff. 

Corrective Actions 

Actions taken when limits 

of control measures are 

not met 

(8) Cease operation and clean 

equipment before launching onto water.

Cease operation and remove all adult zebra 

mussels. Spray boat and equipment with hot 

water (104F) or allow to dry completely for 5 

days prior to entering non-infested waters. 

Verification 

Method of verification 

 

(9) Review records. Review records. 

Records 

List what is recorded at 

each critical control point 

 

(10) Record the procedure used to 

remove plant fragments. Record that 

inspections occurred prior to leaving one 

site and entering the next.

Record the procedure used to remove zebra 

mussels and rusty crayfish. Record that 

inspections occurred prior to leaving one site and 

before entering the next. 

 

This form accommodates 2 Critical Control points. Attach additional pages of this form as necessary. 

 

Final Step: 

Once the HACCP plan is completed, attach it to the signed procedure form with the hazard analysis worksheets 

Standard Operating Procedure #6: 

Field Measurements and Water Sample Collection 

Version 1.0 

In Large Rivers Water Quality Monitoring Protocol 

Prepared by 

Suzanne Magdalene and Daniel Engstrom 

St. Croix Watershed Research Station 

16910 152nd. St. North 

Marine on St. Croix, Minnesota 55047 

and 

Joan Elias (contact author) 

National Park Service 

Great Lakes Inventory and Monitoring Network 

2800 Lake Shore Drive East 

Ashland, Wisconsin 54806 

joan_elias@nps.gov 

August 2008 

Suggested citation: Magdalene S., D.R. Engstrom, and J. Elias. 2008. Standard operating 

procedure #6: Field measurements and water sample collection. in Magdalene, S., D.R. 

Engstrom, and J. Elias. 2008. Large rivers water quality monitoring protocol, Version 1.0. 

National Park Service, Great Lakes Network, Ashland, Wisconsin. NPS/GLKN/NRR—

2008/060. National Park Service, Fort Collins, Colorado.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page ii

Contents 

 Page

Revision History Log..................................................................................................................... iv 

Acknowledgements..........................................................................................................................v 

6.0 Introduction..........................................................................................................................1 

6.0.1 Core Suite of Water Quality Variables ......................................................................1 

6.0.2 Advanced Suite of Water Quality Variables...............................................................1 

6.1 When and Where to Sample ................................................................................................2 

 6.1.1 Safety Concerns ..........................................................................................................2 

 6.1.2 Quality Assurance Concerns.......................................................................................2 

6.2 Equipment and Supplies ......................................................................................................3 

 6.2.1 Instrument Specifications............................................................................................3 

 6.2.2 Additional Equipment, Supplies, Forms, etc. .............................................................3 

6.3 Overview of Field Work ......................................................................................................5 

6.3.1 Sequence of Activities During Field Workday...........................................................5 

6.3.2 Recording Field Information Upon Arrival at Monitoring Site..................................6 

6.3.3 Preventing Contamination ..........................................................................................7 

6.3.4 Using Disposable Gloves............................................................................................7 

6.3.5 Bottle Preparation – Types and Sizes of Bottles.........................................................8 

6.4 River Stage and Discharge...................................................................................................8 

 6.4.1 Visual Observations....................................................................................................9 

6.4.2 Measuring River Stage..............................................................................................10 

6.4.3 Measuring River Discharge ......................................................................................10 

6.5 Taking Field Measurements...............................................................................................11 

6.5.1 Where to Measure Field Variables ...........................................................................12 

6.5.2 Stabilization of Sensor Probe Readings....................................................................12 

6.5.3 Measurement Sequence ............................................................................................13 

6.5.4 Detailed Description and Troubleshooting Hints for Field Variables ......................14 

6.6 Water Sample Collection ...................................................................................................19 

6.6.1 Integrated Sampling Tube.........................................................................................19 

6.6.2 Discrete Depth Sampling ..........................................................................................20 

6.6.3 Dispensing Aliquots into Analyte Bottles.................................................................20 

6.6.4 Sample Preservation..................................................................................................20 

6.6.5 Quality Assurance and Quality Control of Field Duplicates ....................................20 

6.7 Departure from Monitoring Site ........................................................................................20 

6.8 Field Methods Summary....................................................................................................21 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page iii

6.9 Quality Assurance/Quality Control Procedures.................................................................21 

6.9.1 Calibration of Field Instrument Sensors ...................................................................21 

6.9.2 Calculation of Field Instrument Performance Criteria..............................................26 

6.9.3 Quality Assurance/Quality Control Samples............................................................26 

6.9.4 Summary of Quality Assurance/Quality Control Field Procedures..........................28 

6.9.5 Corrective Responsive Action ..................................................................................30 

6.10 Data and Records Management .........................................................................................30 

6.11 Literature Cited ..................................................................................................................31 

Attachments ...................................................................................................................................33 

Field Data Sheet 

 Eureka Manta Calibration Form 

 Eureka Manta Maintenance Form 

 Multiprobe Calibration /Maintenance Log 

Flow Measurements 

Tables 

 Page 

Table 1. Typical sensor performance specifications for field instruments ......................................4 

Table 2. Checklist of field equipment and supplies required for monitoring water quality ............5 

Table 3. Overview of river discharge observation methods and recording frequencies..................8 

Table 4. Overview of core suite water quality variables and sampling frequencies......................12 

Table 5. Recommended instrument stabilization criteria for recording field measurements ........13 

Table 6. Overview of advanced suite water quality variables and sampling frequencies .............19 

Table 7. Ideal calibration frequency and acceptance criteria.........................................................22 

Table 8. Error limits for post-calibration checks ...........................................................................26 

Table 9. Frequency, acceptable range, and corrective actions for duplicate samples ...................28 

Table 10. Summary of QA/QC documentation and sampling methods ........................................29 

Figures 

 Page 

Figure 1. Key features used to identify bankfull discharge .............................................................9 

Figure 2. Schematic diagram of discharge measurement procedure in cross-section ...................11 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page iv

Revision History Log 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project manager must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the header of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log: 

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page v

Acknowledgements 

We consulted protocols written for the U.S. Environmental Protection Agency (Baker et al. 

1997), for the U.S. Geological Survey (Hoffman et al. 2005; USGS 2005), and for other National 

Park Service networks (O’Ney 2005). We also consulted an on-line curriculum for monitoring 

water quality (WOW 2004) and National Park Service internal documents (Penoyer 2003). We 

wish to acknowledge these sources and thank them for the valuable contributions they made to 

this document. We also wish to thank Rich Axler and Elaine Ruzycki for contributing verbiage 

to earlier drafts of this document, and Tracey Ledder for scrutinizing the document for 

inconsistencies in quality assurance/quality control. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 1

6.0 Introduction 

Field measurements should represent, as closely as possible, the natural condition of the 

surface water at the time of sampling. Experience with and knowledge of the sampling 

equipment and the collection, storage, and processing of water samples for subsequent 

laboratory analyses are critical for collecting data of high quality. To ensure consistent, highquality data, always: 

• Make field measurements only with properly calibrated and maintained instruments that 

have been allowed to equilibrate in situ. 

• Maintain a permanent log book for each field instrument for recording calibrations and 

maintenance. Review the log books before leaving for the field. 

• Test each instrument (meters and sensors) before leaving for the field. Verify that 

batteries are fully charged. Become familiar with new instruments and new measurement 

techniques before collecting data. 

• Have backup instruments readily available and in good working condition. 

• Follow quality assurance/quality control procedures. Such protocols are mandatory for 

every data collection effort, and include practicing good field procedures and 

implementing quality-control checks. Make field measurements in a manner that 

minimizes artifacts that can bias the result. Check field-measurement precision and 

accuracy (variability and bias). 

• Keep complete field, sampling, and data handling records, such that anyone using the 

data may trace the sampling history. 

During the selection of vital signs, GLKN and its advisors identified as high priorities ‘core 

suite variables’, which are in situ physical and chemical field measurements, and ‘advanced 

suite variables’, which include laboratory analyses of nutrients, sediments, cations, anions, 

and biota (described in Route 2004). 

6.0.1 Core Suite of Water Quality Variables 

The core field variables are flow, temperature, specific conductance, pH, and dissolved 

oxygen, all of which are mandated by the National Park Service Water Resources Division 

(NPS-WRD). To this mandated suite, GLKN has added a measure of water clarity. Stream 

gage level and discharge will be determined at benchmark stations on a regular basis; methods 

are described in Section 6.4. Depth profiles of temperature, specific conductance, pH, and 

dissolved oxygen will be measured at each sampling station using a multiparameter instrument 

(multiprobe). Water clarity will be measured with a transparency tube or Secchi disk. The 

expected ranges and resolutions required of multiprobes are listed in Table 1, and the methods 

for taking field measurements are described in Section 6.5. 

6.0.2 Advanced Suite of Water Quality Variables 

The advanced suite variables of the large rivers protocol consists of total phosphorus, total 

nitrogen, nitrate+nitrite-nitrogen, ammonium-nitrogen, sulfate, chloride, magnesium, calcium, 

potassium, sodium, dissolved silica, total organic carbon, alkalinity, total suspended solids, and 

total chlorophyll-a. The methods for collecting water samples for these variables are described in 

Section 6.6. These water quality variables were chosen to monitor effects of the leading pressure 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 2

on the resource, land use change toward intense agricultural and urban development. Other 

variables symptomatic of urban development (e.g., volatile organic compounds) are monitored in 

these rivers by regulatory agencies, such as the Minnesota Pollution Control Agency and the 

Metropolitan Council Environmental Services, and GLKN’s bioaccumulative contaminants 

protocol (Route et al., in preparation). 

6.1 When and Where to Sample 

The timing and placement of sample collection are controlled by concerns for: 1) the 

physical safety of field personnel, and 2) the quality assurance of monitoring data. 

6.1.1 Safety Concerns 

6.1.1.1 Season 

Do not collect samples from an ice-covered river – it can be difficult and dangerous, unless 

overhead bridge access is available. For this reason, the GLKN’s monitoring period for large 

rivers is limited to the open-water season, which is approximately March through November in 

the upper Midwest U.S. Each river and reach should be evaluated for safety on an individual 

basis. 

6.1.1.2 Time of Day 

Conduct sampling during daylight hours. Plan field day accordingly, and begin sampling the 

last station of the day well before dusk. However, as a precaution, pack flashlights or headlamps 

for each member of the field team. The boat used for sampling should have safety lights for 

visibility. 

6.1.2 Quality Assurance (QA) Concerns 

6.1.2.1 Sequence of Sites 

Multiple locations on the same river sampled on the same day should be sampled in an upstream 

direction (i.e., the most downstream location sampled first) to minimize disturbances due to the 

sequence of sampling. If there is reason to suspect that part of the resource is contaminated by 

regulatory parameters or invasive species, then conduct sampling from areas of lowest 

concentrations to areas of highest concentrations (this may be from upstream to downstream). 

6.1.2.2 Time of Day 

River water quality can vary in diurnal cycles. When re-visiting sites on a monthly basis, try to 

sample each site at the same time of day as on previous visits. 

 

6.1.2.3 Stabilization of Sensor Readings 

Before making field measurements, properly-calibrated sensors must be allowed to equilibrate 

to the condition of the water being monitored. For details, see Section 6.5.2. 

6.1.2.4 Sample from Flow Centroid 

Whenever possible, collect water samples from the centroid of flow. The centroid of flow is the 

midpoint of streamflow, or the point on the river’s cross-section perpendicular to flow that has 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 3

equal volumes of flow to the right and to the left sides. Sampling from the centroid of flow 

assures that average water quality conditions are being sampled, and that water quality results are 

representative of average flow conditions. 

6.1.2.5 Avoid Sources of Contamination 

For all sampling, it is critical to avoid sampling water showing evidence of oil, gasoline or 

anything else from the boat motor. After setting anchor, allow water flow to clear stream water 

of disturbances. Collect samples on the upstream side of the boat, to minimize contamination 

and disturbance. Avoid surfactants, floating debris, and turbid aeration during sample 

collection. Discard rinse water or excess sampling water on the downstream side of the boat. 

Always follow procedures for minimizing contamination during the sampling process. 

6.2 Equipment and Supplies 

6.2.1 Instrument Specifications 

Toward low bias and high precision of water quality data for this protocol, Table 1 lists typical 

field sensor performance specifications that should be expected from monitoring equipment. 

Multiparameter sensor instruments (or multiprobes), while expensive, are convenient and 

commonly used in water quality monitoring. A multiprobe instrument should be selected based 

on the observable range for each variable. However, an additional investment in a back-up set of 

less expensive individual sensors will help ensure the development of a long-term dataset, 

should the multiprobe not be working properly. 

Instrument-specific estimations of the range of uncertainty for each variable must be calculated 

for use in the interpretation of data. Therefore documentation will be maintained regarding the 

ability of each multiprobe to meet the data quality objectives of this project; blank forms are 

included SOP #12. The completed forms for each multiprobe will be maintained along with the 

calibration and maintenance logs for the multiprobe. Details on estimating instrument sensitivity 

are included in SOP #12, Quality Assurance/Quality Control. Because field equipment is likely 

to change during the course of this long-term monitoring project, QA/QC procedures must be 

followed on documenting cumulative bias (SOP #12). 

6.2.2 Additional Equipment, Supplies, Forms, etc. 

Refer to the checklist of supplies and equipment needed for field sampling (Table 2) prior to 

each sampling trip. Keep on hand all necessary forms, calibration logbooks, field logbooks, field 

data sheets, procedural manuals, and equipment instructional manuals. Copy field data sheets on 

waterproof paper. See the attachments for blank data sheets. The instruction manuals for each 

instrument should be copied and the originals placed in a secure file and kept in the office. 

Specific sections of the manual that might be important to have in the field should be copied onto 

waterproof paper and remain in the field kit. Include copies of a datalogger software manual. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 4

Table 1. Typical sensor performance specificationsa for field instruments (Penoyer 2003). 

Sensor Expected 

Range 

Reporting 

Resolution b Estimated Bias c

Temperature -5 to 45 

°C 0.01 °C ±0.15 °C 

Specific Conductivity 

(SC25) 

0 to 2000 

uS/cm 

1 uS/cm 

(range 

dependent) 

±0.5% of reading + 1 uS/cm 

pH 1 to 14 

units 0.01 unit ±0.2 units 

Dissolved Oxygen 

(Concentration) 

0 to 50 

mg/L 0.01 mg/L 0 to 20 mg/L; ±0.2 mg/L; 

20 to 50 mg/L:±0.6 mg/L 

Dissolved Oxygen 

(% saturation) 

0-200% 0.1% ~ ±2 % 

Depth - Z 

(pressure sensor) 

0 - > 

100m 0.1 m ~ 0.1 m 

Notes: 

a: In the case of field probes, accuracy is typically a best-case maximum deviation from known correct values (typically based on 

comparisons with known NIST certified reference materials or standards). True accuracy is a combination of high precision and 

low bias (see Irwin 2004 for more details). 

b: Resolution/sensitivity is a data quality indicator related to detection limits but typically handled differently for field probes 

than for laboratory parameters. For more information, see Irwin (2004). 

c: Estimated bias specifications reflect the uncertainty in measurement of the instrument and sensor in combination only, and not

other factors that can affect accuracy, such as environmental variables or the ability of field personnel to calibrate and operate the 

instrument using proper protocols. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 5

Table 2. Checklist of field equipment and supplies required for monitoring water quality. 

√ Equipment and Supplies 

 Field notebook, pencils, and pen (waterproof ink) 

 New field forms on waterproof paper 

Up-to-date field folders containing recent data for field comparison (never take originals in 

the field) 

 Multiparameter instrument (calibrated), calibration standards, check solutions, data logger 

 Long and short cables for multiprobe instrument(s) 

 Calibration logbook for each instrument 

 All maintenance parts and calibration standards for field instruments 

Backup instruments in case of electronic failure of multiprobe (for example: YSI 85 [T-DOSC25] or equivalent, armored NIST certified thermometer [°C], portable pH meter) 

 Transparency tube 

 Secchi disk and metered line (marked at 0.5 m intervals) 

 Sounding weight(s) 

 Surveyor’s rod and level 

 Water samplers: Integrating tube, Van Dorn type sampler 

 Compositing jug and other bottles 

 Weather radio or barometer 

 Pocket calculator (waterproof, if possible) 

 Extra batteries for all field equipment (multiparameter probe, calculator, GPS, etc.) 

 Rain gear 

 Personal flotation device(s) 

 Field trip itinerary 

 Cellular phone and/or park radio 

 Digital camera with extra flash cards and battery 

 Map(s) of station location, preferably at different scales 

 GPS unit 

 Deionized or distilled water for field rinsing 

6.3 Overview of Field Work 

6.3.1 Sequence of Activities During Field Workday 

1. Review field gear checklist. 

2. Create a new field form for each monitoring station, printed on waterproof paper. 

3. Prepare sample bottles and labels in advance and place in a cooler. 

4. Conduct daily calibration of appropriate meters and probes. 

5. Inspect motorized field vehicles at the beginning of every field day, including all safety 

and directional lights, oil, gasoline, and tire air pressure levels. 

6. Drive to monitoring site. If sampling from a bridge, set out traffic safety cones. If 

sampling by boat, load boat with sampling gear, launch boat, and navigate to monitoring 

site. Set up a clean work space on the boat for sampling. 

7. Refer to description of monitoring station location, directions, and photo to verify correct 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 6

location. Verify coordinates on GPS unit. 

8. Record observations and/or measurements of river discharge per Section 6.4. 

9. Locate the centroid of flow. Measure field water quality variables per Section 6.5 and 

collect samples per Section 6.6. 

10. Be sure that all samples are correctly labeled and preserved on ice. 

11. Clean sampling equipment per SOP #7. Rinse sensors with deionized water and perform 

calibration re-checks, as detailed in SOP #12. 

12. Verify that field form is completely filled out, and initial the form. 

13. If sampling from more than one monitoring station in a day, follow procedures for 

decontamination of equipment per SOP #5, and go back to step 6, above. 

14. Upon return to shore, inspect boat, trailer, and all equipment that has come into contact 

with the water for invasive species. 

15. Return to office or field station. 

16. Process samples according to SOP #7. Refrigerate or freeze samples, as required and 

package samples for sending to contract analytical laboratory. 

17. Enter field and laboratory data into NPSTORET as soon as possible. 

6.3.2 Recording Field Information Upon Arrival at Monitoring Site 

Consistent methods are important to long-term data quality. In actuality, the ideal conditions are 

not always met in the field or in the lab and changes in staff occur. Therefore, documentation of 

procedures, site conditions, laboratory analysis, and reasons for deviations of any kind is 

important. Personnel are encouraged to write down more than they feel may be necessary in the 

moment, as the future interpretation of their data will depend on the written record and not the 

memory of an individual. Waterproof field forms (copy available in the attachments) should be 

prepared ahead of time labeled with the project and station IDs. Sampling stations will be 

identified by park, waterbody name, and river mile according to GLKN guidance. Information on 

the sampling station and park will comply with NPSTORET requirements. Field sampling forms 

are used to record the physical and chemical water quality variables measured at the time of 

sample collection. In addition to recording the field variables, any samples collected for 

laboratory analyses must be so indicated. Documentation should include calibration data for each 

instrument, field conditions at the time of sample collection, visual observations, and other 

information that might prove useful in interpreting these data in the future. 

While at each monitoring site, the information recorded on field sampling forms should include: 

• Date and day of week 

• Time of arrival 

• Names of field team members 

• GPS coordinates, to verify location 

• Current weather (air temperature and wind speed) and relevant notes about recent 

weather (storms or drought), including days since last significant precipitation 

• Observations of water quality conditions (see below) 

• Multiparameter meter (model/serial no.), calibration date, and field measurements of core 

suite variables 

• Whether any samples were not collected, and reason 

• List of sample IDs and collection times for advanced suite variables or quality assurance 

samples 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 7

• Quality assurance/quality control procedures followed 

• Flow discharge information and measurements (on separate form) 

• Any other required metadata for NPSTORET data entry 

• Time of departure 

All entries should be made clearly. If an incorrect entry is made, a single heavy line should be 

drawn through the incorrect entry and the correction made. All corrections should be initialed 

and dated. The completed field forms will be maintained in chronological order by station, 

copied into project binders and the originals maintained on file indefinitely. Field data are 

reviewed annually by GLKN personnel (see SOP #8, Data Entry and Management, for details). 

Upon arrival at the monitoring station, record visual observations of water quality conditions that 

will be useful in interpreting water quality data. To be consistent and to help orient others to the 

location of observations, the convention left bank/right bank is used. Left bank is defined as the 

bank to the left of the observer when facing downstream, and the right bank is to the right of the 

observer when facing downstream. 

• Water appearance — General observations on water may include: color, unusual amount 

of suspended matter, debris, or foam. 

• Biological activity — Excessive macrophyte, phytoplankton, or periphyton growth. The 

observation of water color and excessive algal growth is very important in explaining 

high chlorophyll-a values. Other observations to note include types of fish, birds, or 

spawning fish. 

• Unusual odors — Examples include hydrogen sulfide, mustiness, sewage, 

petroleum, chemicals, or chlorine. 

• Watershed or in-stream activities — Activities or events that are impacting water quality, 

for example, bridge construction, shoreline mowing, or livestock watering upstream. 

6.3.3 Preventing Contamination 

Field technicians should be aware of and record potential sources of contamination at each field 

site. Decontaminate field sampling equipment according to SOP #5 for minimizing the risk of 

spreading invasive species. Clean field and laboratory equipment according to SOP #7 to avoid 

contamination of analytes to be measured. Do not allow sample water to touch hands; do not 

touch insides of sampling equipment, containers, or laboratory bottles. 

6.3.4 Using Disposable Gloves 

Wearing disposable gloves is strongly recommended when handling acid preservatives. Check 

manufacturer’s chemical resistance information to be sure gloves are appropriate for compounds 

to which they will be exposed. Common glove types include those made of vinyl, latex and 

nitrile; nitrile is in standard use for USGS sampling work because of its resistance to most of the 

chemicals to which it typically will be exposed for the length of exposure (usually < 15 minutes). 

Field personnel are cautioned that direct contact with materials such as latex or nitrile can cause 

severe allergic reactions in some individuals and should be monitored. 

Physical properties to consider when selecting disposable gloves are glove length, slip 

protection, puncture resistance, heat and flame resistance, cold protection and comfort. These 

factors can vary between manufacturers. Gloves should be inspected visually for defects. Check 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 8

for tears, punctures and other flaws that can prevent the glove from being an effective shield. 

After putting the gloves on, rinse them with water while gently rubbing hands together to remove 

any surface residue before handling sampling equipment. 

6.3.5 Bottle Preparation – Types and Sizes of Bottles 

For each monitoring station, select the bottles appropriate for each analyte and label them with 

station ID, sample date, and analyte code according to the requirements of the contact analytical 

laboratory. Store pre-labeled bottles in a dry box or in separate bags for each station. 

6.4 River Stage and Discharge 

Water quality concentrations are affected by fluctuations in flow. Long-term monitoring of river 

water quality requires an understanding and analysis of river discharge. For example, a 

suspended sediment concentration of 1000 mg/L at low flow would represent something entirely 

different than the same value at high or flood flows. A record of discharge enables the 

assessment of flow-corrected concentrations and loading analysis. For this reason, the qualitative 

estimate or quantitative measurement of discharge is required for all freshwater flowing 

waterbodies (Penoyer 2003). NPS-WRD recommends that all long-term monitoring stations be 

equipped with a staff gage, and that flow be measured whenever core suite field variables are 

measured or advanced suite samples are collected. Where available, discharge data from a 

nearby continuous gaging station may be used as a proxy for on-site measurements at monitoring 

stations. Occasional validation of the proxy data should be conducted by comparison with 

discharge measurements at the monitoring site (2-3 times/year). However, in the absence of any 

nearby continuous recording gaging station, it is usually best to install a staff gage (Penoyer 

2003). 

If there is no water flow in the river, leaving isolated, stagnant pools in the river bed, DO NOT 

take measurements or collect samples from a pool; water in the pools will not be representative 

of the water quality of flowing waters. 

There are three methods of recording river discharge information: 1) qualitative description of 

visual observations, 2) water elevation or stage or gage height read from a dedicated staff gage, 

and 3) quantitative measurement of river flow rate using a current meter. Table 3 summarizes the 

frequency with which each method should be employed. Once sufficient data have been 

gathered, field personnel can use a discharge-rating curve for each site that relates stage readings 

to discharges. The rating relationship needs to be verified on a regular basis (2-3 times/year). 

Table 3. Overview of river discharge observation methods and recording frequencies. 

Observation Method Which Sites Recording Frequency 

Visual observation Every site Every visit 

Stage height Those with dedicated staff gage Every visit 

Discharge measurement Those with dedicated staff gage 2-3 times/year 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 9

6.4.1 Visual Observations 

Visual observations are simple but useful pieces of information when assessing water quality 

data. 

Visually inspect the stream from bank to bank and longitudinally, observing velocity, width 

and depth distribution, and apparent distribution of sediment and aquatic biota along the 

cross section. Note and document the location of stagnant water, eddies, backwater, reverse 

flows, areas of faster than normal flow, and piers or other features along the cross-section. 

At a minimum, a qualitative estimate of flow will be made based on visual estimation of 

relative % of bankfull conditions at the time of sampling, as follows (Penoyer 2003): 

Dry: no water or isolated, stagnant pools 

Low: ≤ 25% of bankfull 

Intermediate: 25-75% of bankfull 

High: ≥ 75% of bankfull 

Flood: >100% of bankfull conditions. 

The quality of visual observations is highly dependent on river geometry and the knowledge of 

monitoring personnel. Field personnel need to be experienced or trained in identifying the 

location of the top of the river bank that defines bankfull conditions. It is generally accepted that 

bankfull stage corresponds with the discharge that fills a channel to the elevation of the active 

floodplain. The bankfull discharge is considered to be the channel-forming agent that maintains 

channel dimension and transports the bulk of sediment over time. Field indicators include the 

highest elevation of the tops of sand bars, the highest scour line, significant breaks in crosssectional slope, changes in vegetation, and the top of the channel bank. The Woodyer (1968) 

method best summarizes these features (Figure 1): 1) a low bench level, with a streambed of 

coarse-sized particles that is only exposed under low flows, 2) a middle bench level, representing 

average flow conditions that allow the annual growth of short vegetation, and 3) a high bench 

level (bankfull), representing flow conditions that allow the perennial growth of tall and stout 

vegetation. 

Figure 1. Key features used to identify bankfull discharge (from Woodyer 1968). 
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SOP #6, page 10

6.4.2 Measuring River Stage 

River stage is defined as the water surface elevation relative to an arbitrary zero datum at a given 

location. To measure river stage for the development of discharge rating curves, it is usually best 

to install a staff gage (Penoyer 2003). A staff gage is a scale bar (usually enameled steel) placed 

in a stream to show the elevation of the water surface. The staff gage should be located in an area 

that will provide some degree of protection from floating debris. Mounted on a 4x4 post and 

anchored in the stream bed (or mounted on a bridge), the gage will consist of a vertical scale that 

is permanently marked in increments of 0.01 ft and the stage is read directly from these markings 

to the nearest 0.01 ft. The staff gage is mounted at the time of installation to enable gage readings 

across the expected range of low- to high-flows. As an alternative to a staff gage, stage height 

can be measured from a permanent and stable benchmark, such as a bridge railing or a bedrock 

ledge. In these cases, a tape measure is used to record the water level as the distance below the 

benchmark datum. 

Regardless of the type of gage (staff gage or benchmark), the gage height at zero flow (GZF) 

should be calculated for each gage. For most river cross-sections, GZF is equivalent to the 

lowest elevation of the stream bed, or the measured water elevation minus the deepest partial 

section. The gage height can be calibrated to the global coordinate system by referencing a 

datum on the gage to the surveyed elevation of the water surface, preferably at the time of 

installation. 

6.4.3 Measuring River Discharge 

River discharge is defined as the volume of water per unit time that passes through a river crosssection at a given location, and is commonly measured in cubic feet per second. Discharge 

should be measured when: 

• Verifying a discharge rating curve for the monitoring station (2-3 

measurements/yr), or 

• Comparing discharge measurements with those of a nearby continuous gaging station (2-

3 measurements/yr). 

The basic method for discharge measurement has not changed in several decades and is best 

detailed by the USGS (Buchanan and Somers 1969). A river cross-section is identified and 

marked within a straight reach of river having low turbulence and stable banks. Stage height is 

measured from a permanent gage. The hydrologist divides the cross-section into several partial 

sections, usually 25 or more, depending on the width of the river. At the midpoint of each 

partial section, the flow depth and average flow velocity are measured using a current meter 

with a top-setting wading rod or sounding weight attached to a cable. The average flow 

velocity of each partial section is measured and recorded. Discharge is the product of flow 

velocity and cross-sectional area, so the total discharge of a river cross-section is calculated as 

the sum of the product of the velocity and the area measured at each partial section (Figure 2). 

Dimensions are traditionally measured and reported in English (not metric) units of feet and 

seconds. 
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SOP #6, page 11

Figure 2. Schematic diagram of discharge measurement procedure in cross-section. 

Refer to Magdalene (2008) for details on: 

• Equipment and methods, depending on flow depth 

• Defining the river cross-section 

• Finding lateral positions within the cross-section 

• Measuring flow depth and velocity 

• Recording flow measurements 

• Calculating and reporting flow 

6.5 Taking Field Measurements 

All of the core suite water quality variables shall be measured in situ. Core suite water quality 

variables (described in greater detail in 6.5.4) and their sampling frequencies are listed in Table 

4. In general, core suite variables should be measured: 1) every time advanced suite water quality 

samples are collected (9x/yr), to aid in the interpretation of analytical results, and 2) to confirm 

adequate mixing in the river cross-section whenever the discharge rating curve is verified with 

current meter measurements (2-3x/yr). In the first case, a single vertical profile measured at the 

centroid of flow is required. In the second case, as many as 25 vertical profiles measured at 

subsections of the river cross-section during discharge measurements may be needed (see SOP 

#4 for more details on site establishment). 
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SOP #6, page 12

Table 4. Overview of core suite water quality variables and sampling frequencies. 

 Monitoring Frequency 

Core Suite Variables EPA Method Profile at 

centroid only 

Profiles in 

cross-section 

Temperature (T) 170.1 9x/yr 2-3x/yr 

Specific Conductivity (SC25) 120.1 9x/yr 2-3x/yr 

Hydrogen Activity (pH) 150.1 9x/yr 2-3x/yr 

Dissolved Oxygen (DO) 360.1 9x/yr 2-3x/yr 

Turbidity 180.1 9x/yr 2-3x/yr 

Clarity N/A 9x/yr 2-3x/yr 

6.5.1 Where to Measure Field Variables 

A vertical profile of all core suite variables, except clarity, should be measured simultaneously 

at the centroid flow, defined as the lateral position in the cross-section at which discharge is 

equal on both sides of the sampling point. The location of the centroid can be determined 

directly from the discharge measurement sheet by adding a cumulative discharge column to the 

discharge measurement form. The centroid of flow will be located in the vertical that contains 

50% of the total flow. 

Locate the centroid of flow from discharge measurement or from accurate historical discharge 

measurements. The location of the centroid may vary depending on flow conditions (low, 

intermediate, or high flows). If no previous discharge information is available for the observed 

flow conditions, then discharge should be measured in order to identify the location of the 

centroid. If flow is measured first, care must be taken to let flow disturbances settle and clear 

before deploying a multiprobe instrument or collecting water samples. 

For all sampling, it is critical to avoid sampling water showing evidence of oil, gasoline or 

anything else from the boat motor. It is best to turn off the engine and set the anchor, although 

this may not be possible or advisable in bad weather or with a balky engine. The engine is 

commonly located in the stern of the boat; therefore, the anchor should be secured near the prow 

of the boat, such that strong currents will rotate the stern to the downstream end. After setting 

anchor, allow water flow to clear stream water of disturbances. Collect samples on the upstream 

side of the boat, to minimize contamination and disturbance. Avoid surfactants, floating debris, 

and turbid aeration during sample collection. Discard rinse water or excess sampling water on 

the downstream side of the boat. 

6.5.2 Stabilization of Sensor Probe Readings 

Before making field measurements, properly-calibrated sensors must be allowed to 

equilibrate to the condition of the water being monitored. Sensors have equilibrated 

adequately when instrument readings have stabilized, that is, when the variability among 

measurements does not exceed an established criterion. The criteria for stabilized field 

readings were defined by O’Ney (2005) for a set of three or more sequential measurements 

(Table 5). Although the criteria used by the Greater Yellowstone Network (O’Ney 2005) 

differ from those used in the upper Midwest by the NRRI-UMD group (WOW 2004), the 
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SOP #6, page 13

differences are small in comparison to the true range of variability one might expect in the 

field and with aging instrument sensors. The natural variability inherent in surface water or 

ground water at the time of sampling generally falls within these stability criteria and 

reflects the accuracy that should be attainable with a calibrated instrument. In the case of 

field probes, accuracy is typically a best case maximum deviation from known correct values 

(typically based on comparisons with known NIST certified reference materials or standards). True 

accuracy is a combination of high precision and low bias (see Irwin 2004, 2006 for more details). 

Dissolved oxygen typically requires the greatest amount of time to stabilize. In addition, 

differences in polarigraphic sensor membrane thicknesses, age, and rates of oxygen 

consumption increase the variability of the equilibration time. The longest equilibration times 

will typically occur where dissolved oxygen exhibits a steep gradient (change in DO 

concentration > 5 mg/L) or very low oxic levels (DO concentration < 3 mg/L). Depending on 

the site characteristics and the specific oxygen sensor, 3 to 5 minutes may be required for 

complete equilibration. This time far exceeds what is needed for the other variables, which 

typically stabilize in less than 60 seconds. Observers should only note instrument DO readings 

after the stabilization criteria in Table 5 are met, and then record readings for all variables at 

once. 

Table 5. Recommended instrument stabilization criteria for recording field measurements. 

Standard Direct Field 

Measurement 

Stabilization Criteria 

(O’Ney 2005) 

In situ Multisensors 

Stabilization Criteria 

(WOW 2004) 

Temperature: 

Thermistor Thermometer 

Liquid-in-glass Thermometer 

± 0.2 °C 

± 0.5 °C 

± 0.2 °C (5%) 

Specific Conductivity (SC25): 

When ≤ 100 μS/cm 

When > 100 μS/cm 

± 5 % 

± 3 % 

< 5 uS/cm (10%) 

pH: Meter displays to 0.01 ± 0.1 unit ± 0.2 unit (10%) 

Dissolved oxygen: 

Amperometric (same as 

polarigraphic) method 

± 0.3 mg/L ± 2% ± 0.5 mg/L (10%) 

6.5.3 Measurement Sequence 

Acquiring high quality results requires the use of consistent measurement methods. Use the 

following sequence: 

1. Go to the centroid of flow. Obtain measurements directly from the waterbody by 

immersing the multiprobe instrument, allowing it to equilibrate before measurements are 

recorded. 

2. Measure at multiple depths in the vertical: take first reading at ~0.5 m depth after 

stabilization of the multiprobe. Lower the multiprobe and take stabilized readings at 1.0 
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SOP #6, page 14

m. Thereafter, take stabilized readings every 1.0 m. 

3. When the current velocity is swift and a vertical profile is not feasible without 

compromising the integrity of the multiprobe, limit the profile to a reasonable depth, and 

document field conditions. 

4. Quality Assurance (QA): At a minimum, replicate one of every 10 sets of measurements 

(e.g., at 1 m, 10 m, etc.). The replicate should be taken immediately following the 

original reading. Values should agree within ±10% or the stabilization levels listed in 

Table 5, whichever is larger. 

5. Use the depth-integrating sampler to collect a sample; fill a compositing jug. Use sample 

water from the compositing jug to fill the transparency tube and measure clarity. Ensure 

sample is well-mixed prior to filling the transparency tube. 

6. Refer next to Section 6.6 for the instructions on collecting and storing water samples. 

6.5.4 Detailed Description and Troubleshooting Hints for Field Variables 

Because temperature, DO, and other water quality variables are important determinants of 

biotic habitats, it is important that observers write down values on field forms and think about 

their ecological meaning, even if a data logger is recording the measurements. The hard copy 

also serves as backup in case there is an electronic failure. 

6.5.4.1 Temperature 

Temperature (T) measured in units of degrees Celsius (°C), and recorded to the nearest degree 

or tenth of a degree as warranted by instrument. 

1. If a cabled thermistor is not available, the high specific heat of water allows a temperature 

profile to be obtained by bringing deep samples to the surface with a water sampler and 

immediately measuring temperature with a hand-held thermometer or thermister. Anything 

immersed into the water sampler potentially contaminates that particular sample; a separate 

sample must be collected for water chemistry. 

2. The upper few centimeters of soft sediments are often several tenths of a degree warmer than 

the overlying water. The rise in temperature can be an indication that the probe is submersed 

into the sediments. If this happens, be sure to vigorously shake the instrument in shallow 

water with high DO to clean it before re-taking measurements. Check intermediate depth 

values, and if these values do not meet QA criteria, pull the instrument to the surface and 

clean it. 

6.5.4.2 Specific Conductivity 

Specific conductivity (SC) is the ability of water to conduct an electrical current for a unit length 

and unit cross-section at a certain temperature, measured in units of microsiemens per centimeter 

(μS/cm), and recorded to the nearest μS/cm. Commonly used in water quality monitoring, SC is 

a general measure of the number of ions dissolved in the water. It is important to be aware of the 

difference between SC (specific conductivity at the ambient temperature of the sensor) and SC25 
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SOP #6, page 15

(an abbreviation for specific conductivity temperature compensated to 25°C). This difference 

becomes very important in profiling stratified riverine lakes where the hypolimnion is cold with 

respect to the epilimnion. In such cases, the typical increase in ions with depth, as estimated by 

SC25, would be substantially offset by the corresponding decrease in SC due to decreasing 

temperature. 

The difference between SC and SC25 can confound analyses of seasonal patterns of dissolved 

ions because water temperatures vary throughout the year. The SC25 can be used to monitor 

seasonal changes in total dissolved salts (TDS) such as a spring flush of road salt, which is why 

the temperature compensation is so important. Many instruments will display SC in addition to 

SC25. In the event that an uncompensated sensor must be used (older instruments and most 

pocket conductivity meters are not temperature-compensated), the value of SC25 can be 

calculated from SC and temperature values (see below). 

1. A common physical problem in using a specific conductance probe (or meter) is entrapment 

of air in the conductivity probe chambers. Its presence is indicated by unstable specific 

conductance values fluctuating up to + 100 μS/cm. This artifact is much more prevalent in 

turbulent stream waters and can be minimized by slowly and carefully placing the probe into 

the water and when completely submerged, quickly move it through the water to release any 

air bubbles. An SC probe with an open flow design does not trap air. 

2. Is the value real or is the instrument out of calibration? Having specific conductance 

standards in the field can help verify values that fall outside the expected range. For example, 

the expected specific conductivity is around 200 and the reading is 1500. A known standard 

can be put in the instrument storage cup to determine if the instrument is reading correctly or 

is out of calibration. 

3. SC25 values can be calculated from uncompensated SC values via a temperaturecompensation formula. For example, for YSI probes, use: 

1 0.0191 ( 25) 25+ ⋅ − =

m

m

t

SC SC 

Where, SC25 = corrected conductivity value adjusted to 25°C, 

SCm = measured conductivity before correction; and, 

tm = water temperature at time of SCm measurement. 

Contact the instrument vendor for the appropriate formula. 

6.5.4.3 Hydrogen Ion Activity (pH)

Commonly used in water quality monitoring, pH is a measure of the acidity of water, measured 

in standard pH units (SU), and recorded to the nearest 0.1 pH unit. The pH scale is from 1 to 14: 

neutral water is pH 7, acidic waters have pH <7, and alkaline waters have pH >7. 

• Is the value real or is the instrument out of calibration? Having pH standards in the field 
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SOP #6, page 16

can help verify values that fall outside the expected range. For example, the expected pH 

is around 7.0 and the reading is 9.5. A known standard can be put in the instrument 

storage cup to determine if the instrument is reading correctly or out of calibration. 

• As with dissolved oxygen, a pH probe can take longer to equilibrate to stream water 

when the gradient from the previous measurement is large (>1.0 pH SU). 

• Low ionic strength waters with SC25 < 50 μS/cm can cause pH measurement stability 

problems with some probes. Probes will often calibrate fine in strong ionic strength 

buffers but will not read accurately in lower ionic strength surface waters. If you suspect 

this is the case, use low ionic strength buffers for calibration or use a sensor that is 

designed for low ionic strength waters. 

• Because the pH scale is logarithmic, field values may have to be converted to hydrogen 

ion activity (i.e., concentration) values prior to conducting statistical summaries and 

analyses. Check for normalcy of data. 

o To convert pH value to hydrogen-ion activity, use the equation: Hydrogen 

Activity = 10-pH. 

o To convert the calculated hydrogen ion activity back to pH units, use the 

equation, pH = - log10 (mean hydrogen activity). 

6.5.4.4 Dissolved Oxygen

Dissolved Oxygen (DO)is reported as mg/L and/or percent saturation (% DO). Record values to 

the nearest 0.1 mg/L unless otherwise justified, and to the nearest %. Values measured by 

multiprobes are temperature compensated to 25°C. 

• Be aware that if a water sample has a strong rotten egg smell (H2S gas), it must have a 

DO of zero. This is a good way to check your meter. You can use the measured offset 

value to correct your higher DO values. Do not report negative DO values in the final 

database although it is important to report them on the field data sheet. Do the correction 

afterwards but note on the field sheet the depth at which you could smell sulfide gas. 

• Equilibration time is critical; the steeper the DO gradient, the longer the equilibration 

time. It may take >5 minutes when DO drops abruptly to near zero. 

• The DO probes with Clark cells actually consume oxygen as they work; measurements 

therefore require moving water using either a built-in stirrer (typical in multiparameter 

sondes and BOD probes) or hand jiggling during the measurement. New optical sensors 

do not consume oxygen and hence do not require moving water. 

• If the electronic DO meter is not functioning properly, DO can be measured by Winkler 

titration (APHA 1998). A variety of field kits are convenient and cost effective, including 

Lamotte, Hach, and others.

6.5.4.5 Turbidity

Some multiparameter sondes have a turbidity probe. Even though turbidity is not a core suite 
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SOP #6, page 17

parameter, an explanation is included here for those cases where a turbidity probe is available. 

Turbidity, an optical property of a fluid that describes the amount of light that is scattered by 

suspended solids, is most commonly measured and recorded in nephelometric turbidity units 

(NTUs). Suspended solids, primarily silt and clay, can include finely divided organic and 

inorganic matter, soluble colored organic compounds, plankton and microscopic organisms 

(APHA 1998). Therefore, turbidity is often used as an indicator of the condition and productivity 

of an aqueous system. 

Turbidity measurements are best carried out on site, preferably in situ, to avoid biased results 

from biodegradation, settling, sorption of particulates in the sample, and various precipitates 

caused by changes in sample pH during handling and transport. Therefore, NPSWRD 

recommends the use of submersible turbidity sensors (Penoyer 2003), which operate by directing 

a beam of light from a light-emitting diode into the water and measuring the light that scatters off 

the suspended particles present (Wagner et al. 2000). A submersible turbidity sensor should have 

a measurement range of at least 0 to 1000 NTU, and accuracy better than ± 5 percent should be 

achievable. Sources of bias include water color, gas bubbles, condensation, and scratched or 

dirty sensors. It is recommended to keep the optical windows clear of fouling substances that 

tend to build up and distort turbidity, and wherever possible, to use temperature-compensated 

turbidity sensors. 

In situ measurement of turbidity using multiparameter submersible sensors has generally not 

attained the level of accuracy required in a regulatory environment (e.g., USEPA Method 

180.1). This is particularly true for the higher resolution/sensitivity required in the low end of 

the NTU range in meeting water supply source requirements (0.5 NTU is the legal limit for 

drinking water). According to the USGS Hydrologic Instrumentation Facility, the difference 

relative to standards at the lower range of turbidity measurements (< 20 NTU) can often exceed 

10%. Significant improvements are being made in field turbidity instruments and it is 

recommended that instrument performance be investigated before equipment selection. 

However, for extensive long-term monitoring, where a broad range of conditions occur and cost 

and ease of use are important considerations, the submersible turbidity sensors used in 

multiparameter probes appear to be the most reasonable alternative. 

6.5.4.6 Clarity 

Measurement of Secchi disk transparency has historically been the most common means of 

measuring water clarity due to its simplicity. It is a qualitative evaluation of the transparency of 

water to light based on the reflection of light from the surface of the Secchi disk and is a 

function of the absorption characteristics both of the water and its dissolved and particulate 

matter. To get an accurate measure of Secchi depth, the disk must hang vertically from the side 

of the boat, which is often not possible in flowing systems. The transparency tube, which uses 

the same principle, is recommended in lotic systems. 

Use the following steps to measure clarity with a transparency tube: 

1. Begin with a 120-cm transparency tube. 

2. The tube should be set on a white towel background, shaded by your body, and read 

without sunglasses. 
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SOP #6, page 18

3. Water should be dispensed from a compositing jug that that was used for integrating 

water samples (see below) rather than dipped from the water body. The jug must be well 

shaken prior to filling the tube to minimize artifacts due to settling of sand and larger silt 

particles. Allow air bubbles to disappear before making the final measurement. 

4. While slowly releasing water from the bottom of the tube via its valve, note and record 

the depth to the nearest 0.1 cm at which the mini-secchi first becomes visible. Continue 

releasing waster until the white screw in the center of the mini-secchi becomes visible: 

record this reading. Take the average of the two readings. 

5. Several attempts to read the clarity may be necessary because of overshooting the 

endpoint, so collect plenty of water for this analysis. A standard 120 cm x 4.5cm outside 

diameter tube requires approximately 1.5 L to fill it, so dedicate at least 4 L of water for 

this measurement. 

6. During clear water periods, the tube may not be long enough for the water to extinguish 

sight of the mini-secchi. In this case, the value should be recorded as >120 cm. If it 

appears to be barely visible, this fact should be recorded to distinguish it from a 

measurement where it is clearly visible. 

7. Replicate transparency tube readings at every tenth site for quality assurance. Values 

should agree to ±10%. 

Maintenance notes and other precautions 

1. The rubber stopper (with attached secchi) can be dislodged easily. Tape the stopper with 

black vinyl electrical tape and carry an extra stopper-secchi. 

2. Clean the transparency tube periodically with mild dish soap and a soft cloth. 

3. Although water from the tube may be saved for turbidity and TSS measurements, do not 

save it for nutrient or other pollutant analyses because the tubes are not cleaned according 

to certified protocols. 

4. Subsampling and settling issues are important, as particles settle quickly. A stopper for 

the top of the tube is useful to allow for agitation and resuspension during the 

measurement if rapid settling occurs. 

5. Dissolved color due to organic matter (humic and fulvic acids, usually from bogs and 

conifer needles) can confound comparisons of transparency tube data between monitoring 

stations. Also, water bodies with similar concentrations of suspended sediments can have 

different transparency because smaller particles scatter more light. 

6. A transparency reading taken from one tube cannot be compared with a reading taken 

from another tube made by a different manufacturer if the dimensions are different. 
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SOP #6, page 19

6.6 Water Sample Collection 

Advanced suite water quality variables and their sampling frequencies are listed in Table 

6. Required analytical methods are detailed in SOP #7, Water Sample Processing and 

Analytical Laboratory Requirements. 

Table 6. Overview of advanced suite water quality variables and sampling frequencies. 

Variables Monitoring 

Frequency 

Nutrients (total phosphorus [TP], total nitrogen [TN], 

nitrate+nitrite-nitrogen [NO3+NO2-N], and ammoniumnitrogen [NH4-N]) 

9x/yr 

Major anions (sulfate [SO4

-

], chloride [Cl-]) 3x/yr 

Alkalinity 3x/yr 

Major cations (magnesium [Mg+2], calcium [Ca+2], sodium 

[Na+

], and potassium [K+]) 3x/yr 

Dissolved Silica (SiO2) 3x/yr 

Dissolved Organic Carbon (DOC) 3x/yr 

Total Chlorophyll-a 9x/yr 

Total Suspended Solids (TSS) 9x/yr 

6.6.1 Integrated Sampling Tube 

1. Rinse compositing jug 3 times before sampling. Increase surface water flushing to 6 

rinses if the compositing jug previously contained water that was contaminated with 

sediment or water deemed to have much higher nutrient levels. 

2. Remove both stoppers from integrated sampler. Rinse the integrated sampler in river 

water 3 times (lower to 2 m, raise, lower again, etc. for 3 rinses). 

3. Collect sample by lowering sampler into water column (if water depth will allow it). If 

the site is too shallow for the 2 m sampler, then use one of the following methods: 

o collect sample by using the integrated sampler on an angle instead of vertically, 

o fill jug with 0.5 m deep water using the Van Dorn/Niskin sampler, 

o or fill jug via surface grab. 

Secure the top stopper, raise the sampler vertically, and immediately drain it into the 

rinsed compositing jug. The sampler will start releasing its water as soon as it clears the 

water surface. Two or three integrated samplers of water will be needed to fill a 6 L jug. 

Fill the jug at least 75% full to ensure adequate water for all analyses; if a transparency 

tube measurement will be done, an entire jug is needed. Extra water simply reduces 

variance associated with the site. 
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SOP #6, page 20

4. Once water is collected, immediately begin dispensing it into appropriate analyte bottles 

or keep jug cold and dark until processing in the park lab or home base at the end of the 

day (details below). 

6.6.2 Discrete Depth Sampling 

During the mid-summer sampling when riverine lakes are thermally stratified, (defined as a 

gradient of ≥ 1 °C/m or DO levels ≤ 2 mgO2/L), collect two separate samples.

Collect surface water with the 0 - 2 m integrated tube sampler as above; collect near-bottom 

water with Van Dorn or Nisken sampler from approximately 0.5 to 1 m above the river bottom. 

Because the hypolimnetic water will be used for nutrient analyses only, a smaller container (1 or 

2 L) may be used for storage and transport to the sample processing site. 

6.6.3 Dispensing Aliquots into Analyte Bottles 

Processing water samples and filling analyte bottles may be done in the field or back at the 

field station. See SOP #7 for more details on sample handling and processing. Regardless of 

where handling occurs, the following instructions apply. 

Prepare bottles and labels prior to field sampling. Keep compositing jug with water sample cold 

and dark until ready for processing; a cooler with ice works well. Always ensure sample water in 

the compositing jug has been agitated prior to filling analyte bottles. Rinse the laboratory bottle 

once with sample water if the bottle is not pre-preserved. Some analyses require preservation of 

the sample with acid, which may be added to the bottle by the contract laboratory; in these cases 

do not rinse the bottle first. Take care not to overfill the bottle if the bottle is pre-acidified, as 

overfilling will flood the acid out of the bottle. If the samples requiring acid preservation are not 

pre-preserved, use caution to add the ampule of preservative supplied by the lab and immediately 

rinse hands in water if acid is spilled. Protective gloves are recommended. 

6.6.4 Sample Preservation 

Store water samples in cooler with ice until return to home base for further processing. 

Keeping the bottles in bags, surrounded by but not in the ice, will help preserve label 

legibility. 

6.6.5 Quality Assurance and Quality Control of Field Duplicates 

Collect a field duplicate approximately every 10 samples, or at least once per sampling round. 

Label the replicate analysis bottles with the appropriate code for the replicate (this may vary by 

park), and fabricate a date and time of sampling. Indicate on the field form which monitoring site 

is the replicate, the true sampling time and date, and the fabricated time and date. Treat the 

replicate as a regular sample for all phases of collection, processing, and analysis. See section 

6.9.3, below, for more details on field duplicates. 

6.7 Departure from Monitoring Site 

Before leaving the monitoring site, all field forms, discharge measurement forms, and sample 

labels must be reviewed for legibility, accuracy, and completeness. Any changes in procedure 

due to field condition must be explained in the comments section. Make sure the information is 
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SOP #6, page 21

complete on all forms. Record departure time on the field form. After reviewing each form, 

initial the upper right corner of each page of the form. Document any photos taken by 

including the photo number and roll number or digital camera photo number on the field form. 

6.8 Field Methods Summary 

• Test, calibrate, and check field equipment before going into the field. 

• Allow sensors to equilibrate with ambient water. Always wait for the DO sensor to 

equilibrate prior to sampling, because it takes the longest to equilibrate. 

• Manually record data on waterproof paper, even if the instrument has a data logger. Note 

any abnormalities or qualifications to the data. 

• Always examine the data while in the field. If a measurement does not make sense 

hydrologically in comparison with previous data from that site, then re-measure it 

immediately to help address the problem. 

6.9 Quality Assurance/Quality Control (QA/QC) 

QA/QC basically refers to all those things good investigators do to make sure their 

measurements are right-on (accurate; the absolute true value), reproducible (precise; 

consistent), and include good estimates of uncertainty. It specifically involves following 

established rules in the field and lab to assure everyone that the sample is representative of the 

site, free from outside contamination by the sample collector (no dirty hands touching the 

water), and that it has been analyzed following standard QA/QC methods. 

6.9.1 Calibration of Field Instrument Sensors 

Instrument calibration is an essential part of quality assurance. Table 7 summarizes the ideal 

calibration frequency and minimum acceptance criteria for these sensor probes. The reality of 

logistical constraints at back country sites may preclude calibration and checks of calibration at 

the ideal frequency. This SOP provides only generic guidelines for equipment use and 

maintenance. A wide variety of field instruments are available; such instruments are 

continuously being updated or replaced using newer technology. Keep equipment 

manufacturers' maintenance and calibration instructions for all instruments for reference 

purposes. Field personnel must be familiar with the instructions provided by manufacturers. 

Contact manufacturers for answers to technical questions. 
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SOP #6, page 22

Table 7. Ideal calibration frequency and acceptance criteria. 

 

Parameter USEPA 

Method 

Minimum Calibration Frequency and 

QC checks 

Acceptance 

Criteria Corrective Actions 

Temperature 

thermometer 

or thermistor: 

170.1 Annually, 2-point check with NIST 

thermometer 

 

±1.0 oC 

Re-test with a different 

thermometer; repeat 

measurement 

Specific 

Conductance 

(SC25) 

120.1 Daily, prior to field mobilization; 

calibration check prior to each round 

of sampling 

10% of the readings taken each day 

must be duplicated or a minimum of 1 

reading if fewer than 10 samples are 

read. 

±5% 

RPD 10% 

Re-test; check low battery 

indicator; use a different 

meter; use different 

standards; repeat 

measurement 

pH 150.1 Daily, prior to field mobilization (two 

buffers should be selected that bracket 

the anticipated pH of the water body to 

be sampled with an independent third 

buffer selected to check instrument 

performance in that range); 

Calibration check w/ third buffer prior 

to each round of sampling 

10% of the readings taken each day 

must be duplicated or a minimum of 1 

reading if fewer than 10 samples are 

read. 

±0.05 pH unit 

±0.1 pH unit 

RPD 10% 

Re-test; check low battery 

indicator; use different 

standards; repeat 

measurement; don’t move 

cords or cause 

friction/static 

 

Dissolved 

Oxygen 

360.1 Daily, prior to field mobilization; 

check at the field site if elevation or 

barometric pressure changed since 

calibration 

0.2 mg/L 

concentration 

or 

±10% 

saturation 

Re-enter altitude; re-test; 

check low battery indicator; 

check membrane for 

wrinkles, tears or air 

bubbles; replace 

membrane; use a different 

meter; repeat measurement; 

allow more time for 

stabilization 

Depth -- Daily, prior to field mobilization, 

check at the field site. Check annually 

against commercially purchased brass 

sash chain labeled every 0.5 m to 

ensure that it reads zero at the surface 

and varies <0.3 m for depths <10 m 

and no more than 2% for greater 

depths. 

±0.1 m 

Retest, check low battery 

indicator; repeat 

measurement; use with 

accurately calibrated line 

Transparency 

tube 

-- Transparency tubes have a 100 or 120 

cm scale; ensure tube is clean 

±1.0 cm for 

transparency 

tube 

Clean tube with mild 

detergent and bottlebrush 

 

Marked lines 

(e.g., Secchi, 

Van Dorn) 

-- Check markings annually against brass 

sash chain. If lines are heated (for 

decontamination) check prior to each 

round of sampling. 

±1%, 0–10 m 

±2%, >10 m 

Re-mark line. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 23

6.9.1.1 Instrument Calibration and Maintenance Logbooks

Calibration and maintenance logs for multi-parameter sondes and all back-up sensor probes will 

be maintained and will document the frequency of calibration, maintenance, and calibration 

checks. See the attachments for a blank calibration log form. Keep calibration logs with each 

instrument during the sampling season. Logs will later be archived at the Network office in 

Ashland, Wisconsin. A new log will be started for each field season. Each instrument will have 

a logbook for recording all maintenance and calibration information, including: 

• Serial number, date received, manufacturer’s contact information, especially technical 

service representatives; 

• Service records, dates of probe replacements; 

• Maintenance records, for example, whenever the following general maintenance occurs: 

DO membrane replacement, pH reference probe junction and filling solution, probe 

cleanings, sonde (the sensor housing) replacement, impellor replacement or cleaning, etc. 

• Calibration dates and calibration data; 

• Any problems with sensors. 

6.9.1.2 Handling of Calibration Standard Solutions

Store all calibration standards in a temperature-controlled environment. Standards should be 

dated upon receipt and upon opening. Commercially-purchased calibration standards come with 

an expiration date that must be observed. Ensure that calibration standards are not used beyond 

expiration dates. 

Properly dispose of all waste materials. Used calibration solutions, in general, may be rinsed 

down a sink with water after consideration of the wastewater treatment system available to that 

sink. Material Safety Data Sheets (MSDS) which are sent with manufacturer purchased 

calibration solutions should be kept on file. These documents describe the flammability, toxicity, 

and other safety hazards of reagents. Some reagents may include constituents toxic to aquatic 

life. These should not be rinsed down a sink in any large quantities in primitive areas where the 

ultimate destination of wastewater is the aquatic environment. Instead, these reagents should be 

collected in a properly-marked leak-proof container for disposal in an adequate treatment system. 

6.9.1.3 Temperature

Temperature is typically not adjustable on an electronic sensor but should be crosscompared to a National Institute of Standards and Technology (NIST) calibrated 

thermometer at the beginning and end of each field season, as follows: 

• Compare against a NIST-certified ot NIST-traceable thermometer at a broad range of 

temperatures, for example 0 to 40 °C; 

• The sensor should read within ± 1.0 °C of the NIST thermometer; 

• Typically you cannot adjust the instrument to calibrate it but check the manual to be sure. 

It is a good idea to check the instrument at 0 °C in slurry of ice-water if a calibrated 

(NIST) thermometer is not available since electronic and non-electronic temperature 

sensors are typically linear over the likely range of field temperatures. 

An armored glass thermometer (stored in a PVC tube padded with insulation) that has been 

referenced to the NIST standard should be taken into the field for air temperature and surface 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 24

water temperature measurements and for checks of the electronic sensor. 

6.9.1.4 Specific Conductivity

Specific conductivity (SC25) will be calibrated using a KCl solution as specified by the 

instrument manual. Stock calibration solutions can be purchased commercially, prepared by a 

water quality contract lab, or made in an academic or agency lab. If the KCl solution is prepared 

by an academic or agency lab, it should be cross checked by an external certified lab. Set the 

instrument to record temperature-compensated SC (SC25) rather than SC. 

Because the typical modern SC25 sensor is linear to <3% over the range from approximately 20 

to 10,000 μS/cm, a single point calibration is typically sufficient. A typical standard is 1000 or 

1413 μS/cm. Pre-mobilization error checks of this sensor using 10, 100, 1413, and 10,000 uS/cm 

standards may be used to establish sensor error over the range of most interest in freshwater 

work. 

6.9.1.5 pH

The pH is calibrated using the standard two buffer technique, using either pH 4 and pH 7, or pH 

7 and pH 10, depending on the expected field values. Calibrate the probe according to the 

manufacturer’s recommendations, usually starting with pH 7 buffer followed by the second 

buffer. If a water body is classified as low acid neutralizing capacity (ANC) acid-sensitive (i.e., 

ANC approximately 100 ueq/L or lower), it should also be checked against a low ionic strength 

buffer (LISB) with pH approximately 4, as per protocols from the National Acid Precipitation 

Assessment Program (NAPAP 1990). A low ionic strength pH combination electrode may be 

necessary to acquire this extra level of sensitivity. 

6.9.1.6 Dissolved Oxygen

Dissolved oxygen (DO) is typically air-calibrated, requiring current barometric pressure. It 

assumes that the dry sensor will read 100% saturation in an enclosed airspace with enough 

water in the bottom of the container to saturate the air with water vapor. Temperature also 

affects the saturation as does the air pressure, which varies with elevation and ambient weather. 

Typically, one can assume the barometric pressure to vary with elevation, but some additional 

accuracy may be gained by either using a calibrated barometer, or consulting the local weather 

bureau or airport. Some multiparameter sondes have the capability to measure barometric 

pressure. 

6.9.1.7 Depth 

The length measurement of brass Secchi chains, transparency tubes, and depth sounders usually 

require little calibration after purchase and an initial check for accuracy. Compare all depth 

cables to each other and ensure they are synchronized. A brass Secchi chain can be used to 

calibrate other cables and lines. The use of a brass chain is particularly important because this 

single tool is likely to provide consistent long-term data. Nylon and certain braided weave ropes 

and cords can stretch as much as 20% and may vary depending upon wetness, load, and age. 

Lines may also shrink, as when they are soaked in hot water to avoid spread of exotic species. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 25

Electronic depth sensors, or pressure transducers, are based on pressure differences and must be 

set to zero at the water surface initially. Perform this zero check at every station; however, verify 

the depth measurement with labels on the actual instrument cable. 

A useful and widely-used labeling system for coding depths is: 

1. 5 m increments: Wrap vinyl tape of a specified color at 5 m increments and add an extra 

wrap every 5 m. Therefore, there is a single wrap at 5 m: two wraps at 10 m separated by 

~ 0.5 cm with 10 m lying exactly between the wraps; three wraps at 15 m with the 15 m 

depth located at the middle of the second wrap, and so on. A permanent marking pen 

should be used to write the actual depth on the tape. 

2. 0-10 m depth: Use a second color to make wraps at 1 m intervals to best define shallow 

water columns. 

3. 10-20 m depth: Use the second color, or new third color, to wrap at 2m intervals. 

4. >20 m: Mark the line at 2.5 m intervals or continue with 2 m intervals. 

6.9.1.8 Post-Field Calibration Checks

Post-calibration checks must be performed after each use of the instrument and before any 

instrument maintenance. The sooner this procedure is performed, the more representative the 

results will be for assessing performance during the preceding field measurements. 

Calibration and post-calibration should be no more than 24 hours apart. Take the same care 

used in performing the initial calibration by rinsing the sensors and waiting for sensors to 

stabilize. After making measurements at the last station, fill the sampling cup with ambient 

water (not deionized or tap water). Repeat the initial calibration procedures performed before 

the sampling trip. Record the post-calibration values in a calibration logbook (generally on 

the same page with the initial calibration for that sampling trip). Deviation beyond the 

manufacturer’s specifications is cause for concern and should be addressed before the next 

sampling date. 

Do not adjust the instrument (using calibration controls) 

during the post-calibration check. 

The purpose of the post-calibration is to determine if the instrument has held calibration during 

the day of sampling. Compare the post-calibration values to the expected values for the 

standards. This will ensure that the field measurements for the day can be reported with 

confidence. The difference between the post-calibration value and expected standard value can 

be used to indicate both calibration precision and instrument performance. 

If post-calibration values (Table 8) fall outside the error limits for DO, pH, and specific 

conductance, data collected do not meet quality assurance (QA) standards and should be flagged 

appropriately (see SOP #12 for more details on QA/QC). Measurements may be repeated with a 

different or back-up instrument. If post calibration measurements do not consistently fall within 

the error limits after in-house trouble shooting, the instrument should be returned to the 

manufacturer for maintenance. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 26

Table 8. Error limits for post-calibration checks. 

Parameter Value 

Temperature ± 1 °C, annual calibration check 

Specific Conductance ± 5% 

pH ± 0.1 standard units 

Dissolved Oxygen ± 0.2 mg/L, ± 10% saturation 

6.9.1.9 Sensor Maintenance and Storage

Most multiparameter sondes should be stored with a small amount of water in the storage cup. 

Refer to the manufacturer’s manual for tips on cleaning the probes and housing, routine 

maintenance procedures, and proper storage procedures. 

6.9.2 Calculation of Field Instrument Performance Criteria 

Performance of field instruments must be checked in several ways, as detailed in the QA/QC 

procedures of SOP #12. Formulae for calculating instrument sensitivity, instrument precision, 

instrument bias, and cumulative bias are found in SOP #12. Documentation of these 

performance criteria include estimation of the limits of detection of the multiprobe, the relative 

percent difference of duplicates, measurement of reference solutions, and estimates of change 

due to change in methods or instrumentation. 

6.9.3 Quality Assurance/Quality Control Samples 

Quality control samples are commonly used in documenting quality control associated with the 

collection of samples in the field. Field blanks and duplicates are routinely incorporated into a 

monitoring program without a good understanding of their function. The purpose of these 

samples is to validate the precision and accuracy of laboratory data, and to determine the 

adequacy of preservation techniques, equipment cleaning and preparation, and sampling 

procedures. Field blanks are used to measure and quantify the amount of contamination from 

extraneous sources (preservatives, sample bottles, sample handling, automatic samplers, etc.) 

that might compromise the integrity of a sample (alter its true value or concentration). 

6.9.3.1 Equipment Blanks 

Blanks are an integral part of quality control (QC) and are required for all sampling activities. 

Their creation should be noted in the field log book. Blanks establish that there is no sample 

contamination from the containers during custody, transportation, and or pre-analysis 

preparation either in the field or in the laboratory. Blanks establish the level of constituents 

introduced into a sample by the equipment used for sampling, preservatives, and/or containers. 

We will conduct equipment blanks prior to each field season and occasionally during the field 

season between field sites to ensure field rinsing is adequate. 

Collect an equipment blank prior to the field season as follows: 

1. Clean all equipment used to collect, store, and process water samples (e.g., integrating 

sampler, compositing jug, filtering apparatus) according to SOP #7. 

2. Rinse the equipment used to collect and store water samples (integrating sampler and 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 27

compositing jug) with laboratory reagent grade water three times and discard. 

3. Fill the integrating sampler with a fourth aliquot of laboratory reagent grade water and 

handle and process this aliquot as if it were a river sample to be analyzed. 

Another source of systematic error is sample cross contamination from field sampling 

equipment used to handle a multiple number of samples. The integrated sampler and 

compositing jugs are to be rinsed in the field three times at each site prior to taking a sample. 

Either piece of equipment may be a source of cross contamination. Collect periodic 

equipment blanks as follows: 

1. In between sample sites, rinse the equipment used to transfer water samples (integrating 

sampler and compositing jug) with laboratory reagent grade water three times and 

discard. 

2. Fill the integrating sampler with a fourth aliquot of laboratory reagent grade water and 

handle and process this aliquot as if it were a river sample to be analyzed. 

This sample is labeled as an equipment blank; information is kept on a datasheet describing the 

source of the blank. Results for all parameters should be non-detect. This type of blank is a 

check for cross contamination between sampling sites and control for bias introduced by cross 

contamination. 

Other types of blanks will be used as needed: field sampling conditions or ambient blanks, if 

there is any reason to suspect that ambient air pollution has the potential to contaminate water 

quality samples; preservative blanks, if there is any reason to suspect that a preservative may 

be contaminated; or bottle blanks, any time sample collection bottles are of uncertain quality or 

cleanliness or from a source not previously used. 

6.9.3.2 Sampling Duplicates

The purpose of a duplicate sample is to estimate the inherent variability of a procedure, 

technique, characteristic or contaminant. Duplicate samples are collected and duplicate 

analyses may be made in the field: 1) as a form of field quality control; 2) to measure or 

quantify the homogeneity of the sample, the stability and representativeness of a sample site, 

the sample collection method(s) and/or the technician’s technique. 

Duplicates are analyzed in the laboratory for the same parameters as the monitoring sample to 

which they apply. Laboratory duplicates that exceed QA/QC standards for the parameter are 

retested. Analytical results of duplicate samples will, theoretically, be the same. Realistically, 

results may differ due to the non-homogeneity of the sample source, and sampling and analytical 

errors. Duplicate samples also document the technique and ability of the technician and analyst 

to produce representative water quality data. 

The laboratory analytical report must show test results for the duplicates, blanks, and 

spikes; the analytical method used; and the results for calculations of summary quality 

control statistics. Copies of these reports are a permanent part of the site file. 

Duplicates will ideally be splits of homogeneous samples to estimate measurement precision in 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 28

the context of repeatability unless otherwise documented and justified. If enough sample water 

cannot be collected in the compositing container to facilitate a split sample, then duplicate 

samples will be co-located. 

Duplicate field samples must be collected every sampling trip for each type of sample 

collected and the results must have a Relative Percent Difference (RPD) less than or equal to 

the guidelines in Table 9. Required field parameter measurements can be duplicated to 

estimate the precision of the equipment. Every tenth measurement may be duplicated, and the 

results of both measurements recorded and evaluated as a RPD. The result can be compared 

with the stated precision of the instrument. 

Table 9. Frequency, acceptable range, and corrective actions for duplicate samples. 

Type of 

Duplicate 

Frequency Acceptable Range for 

Precision 

Corrective Action 

Field 

duplicates 

(samples) 

Minimum of 1 per 

trip per parameter 

or 10% of all 

samples per 

parameter per day 

Chlorophyll-a, TSS 

and nutrients ± 30% 

RPD; all other 

parameters ±15% 

RPD 

Audit field personnel and verify 

sample collection procedure; 

resample; reanalyze; revise SOP; 

audit and train field personnel; project 

manager determines whether 

associated data is usable 

Field 

duplicates 

(multiprobes) 

Minimum of 1 per 

trip per parameter 

or 10% of all 

samples per 

parameter per day 

All parameters ±10% 

RPD 

Re-calibrate instrument; replace 

batteries; perform instrument field 

check with different standards; repair 

or replace instrument; notify 

management; audit and train field 

personnel; project manager 

determines whether 

6.9.4 Summary of Quality Assurance/Quality Control Field Procedures 

Quality assurance protocols are means to ensure data collected are as representative of the 

natural environment as possible. Quality assurance procedures are required in all data collection 

efforts as part of this monitoring protocol. Many of the key elements of quality assurance have 

been included in the SOPs where appropriate, as well as detailed in SOP #12. A summary of 

important QA/QC procedures follows. Table 10 lists additional requirements for QA/QC 

methods and documentation. 

• Field staff must be trained by an expert hydrologist(s). Training will include classroom 

time as well as field and lab components. Details of the training are given in the Standard 

Operating Procedure #2: Training and Safety. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 29

Table 10. Summary of QA/QC documentation and sampling methods. 

Procedure Description/reason 

Instrument calibration logs 

Each instrument must have a log in the form of a permanently bound 

logbook. Calibration schedule must be observed, using fresh 

calibration standards. 

Office binder 

Containing: Protocol and all SOPs, checklist of QA/QC reminders, 

copies of equipment calibration and troubleshooting instructions, 

ASR and COC forms, blank field forms. 

Field binders 

Containing: GPS coordinates for verification of correct sampling 

location, maps, directions to sites, table of previous field 

measurements to compare with new measurements 

Field forms 

Field forms are the only written record of field measurements, so 

copies are placed in site binders and originals must be kept on file 

indefinitely. 

Field instrument methods Require consistent measurement methods and detection limits 

Sample preservation and 

minimum holding time 

Concentrations of water quality variables are maintained as close to 

sampling conditions as possible. 

Chain-of-custody 

A chain-of-custody includes not only the form, but all references to 

the sample in any form, document or log book which allow tracing 

the sample back to its collection, and documents the possession of 

the samples from the time they were collected until the sample 

analytical results are received. 

Laboratory methods Require consistent analytical methods and detection limits 

• Use calibrated instruments for all field measurements. Test and/or calibrate the 

instruments before leaving for the field. Each field instrument must have a permanent log 

book for recording calibrations and repairs. Review the log book before leaving for the 

field. 

• All manually recorded field measurement data will be collected on field forms; data that 

are automatically recorded will be captured electronically and the equipment used will be 

documented on field forms. Hard and electronic copies will be made as soon as possible 

after surveys and kept at a separate location as backup. 

• Complete records will be maintained for each uniquely identified sampling station and all 

supporting metadata will be recorded appropriately (field forms or electronically). 

• Make field measurements in a manner that minimizes artifacts that can bias the result. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 30

• Check field-measurement precision and accuracy. Follow the procedures in SOP #12. 

• Collect 10% duplicate water samples; conduct duplicate measurements of field 

parameters at approximately 10%. 

• Create field blanks prior to the beginning of each field season and periodically 

throughout the season. 

6.9.5 Corrective Responsive Action 

The project manager, in consultation with experienced professionals, will be responsible for 

taking corrective responsive action in the case in which QA/QC is not followed or in the case of 

an unexpected event. Responsive action is often needed in the event of broken sample bottles, 

missing data, errors on field sheets, changes due to field conditions, problematic analyses and 

other events that do not fall within the standard operating procedures. A “Memo-to-file” will be 

used to document any decisions or corrections that are made. This memo will include the date, 

name of author, site or sample referred to, a description of the problem or error and a statement 

describing the decision made or action taken. The memo will be archived with the appropriate 

site data and files. 

6.10 Data and Records Management 

• Hand-written field sheets with core suite profiles should be reviewed for completeness 

prior to leaving the site. Make photocopies as soon possible and file them appropriately. 

Download and back up data from the multisensor datalogger as soon as possible. 

• Ensure that field forms, field notebooks, and other hardcopy records are secure, 

organized, and available for viewing, reproduction, or transfer upon request and/or at the 

end of each field season. 

• Schedule and perform regular data transfer and backup. Data will be protected from loss 

or damage by daily backup, when possible, or on a feasible schedule approved by the 

project leader and the data manager. Ideally, raw data are backed up off-site as soon as a 

sampling trip is completed. 

• Record and verify observed or measured data values. Complete paper forms and enter 

data into NPSTORET and/or other electronic databases. 

• A ‘Memo-to-file’ will be used to document any decisions or corrections that are made. 

This memo will include the date, name of author, site or sample referred to, a description 

of the problem or error, and a statement describing the decision made or action taken. 

The memo will be archived with the appropriate site data and files. 

• Data validation, the process by which data is proven or disproved to be accurate, involves 

the review of the results of all measurements, samples, and QC samples. Sample data 

should be flagged if the analyte was detected in a blank at a concentration similar to that 

in the sample; flagged data contain much more uncertainty than unflagged data. Some 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 31

investigation into the sampling method may be needed if flagged data are a continual 

occurrence. 

• Refer to SOP #8 for more details regarding data entry and management. 

6.11 Literature Cited 

APHA (American Public Health Association). 1998. Standard methods for the examination 

of water and wastewater. 20th ed. Clesceri, L.S., A.E. Greenberg, 

A.D. Eaton, editors. Washington, D.C. American Public Health Association. 

Baker, J. R., D. V. Peck, and D. W. Sutton, editors. 1997. Environmental monitoring and 

assessment program surface waters: Field operations manual for lakes. EPA/620/R97/001. U.S. Environmental Protection Agency, Washington D.C. 

http://www.epa.gov/emap/html/pubs/docs/groupdocs/surfwatr/field/ 97fopsman.html 

Buchanan, T. J., and W. P. Somers. 1969. Discharge measurements at gaging stations. United 

States Geological Survey Techniques in Water-Resources Investigations Book 3 

Chapter A8. http://water.usgs.gov/pubs/twri/twri3a8

Hoffman, R. L., T. J. Tyler, G. L. Larson, M. J. Adams, W. Wente, and S. Galvan. 2005. 

Sampling protocol for monitoring abiotic and biotic characteristics of mountain ponds 

and lakes. Chapter 2 of Book 2, Collection of Environmental Data, Section A, Water 

Analysis Techniques and Methods 2-A2. U.S. Department of the Interior, U.S. 

Geological Survey, Reston, Virginia. 

Irwin, R. J. 2006. Draft Part B lite (Just the Basics) QA/QC Review Checklist for Aquatic Vital 

Sign Monitoring Protocols and SOPs, 62 pp., National Park Service, Water Resources 

Division. Fort Collins, Colorado, distributed on Internet only at 

http://www.nature.nps.gov/water/Vital_Signs_Guidance/Guidance_Documents/pa 

rt_b_lite_05_2005.pdf 

Irwin, R. 2004. Vital signs long-term aquatic monitoring projects, planning process steps: Part B, 

issues to consider and then document in a detailed study plan that includes a quality 

assurance project plan (QAPP) and monitoring “protocols” (including standard operating 

procedures), January 2004 draft. Available from: 

http://science.nature.nps.gov/im/monitor/protocols/wqPartB.doc 

Magdalene, S. 2008. Site establishment for large rivers water quality monitoring: Stagedischarge 

relationships at selected sites within the St. Croix National Scenic Riverway. National 

Park Service, Great Lakes Inventory and Monitoring Network Report GLKN/2008/02. 

Available at: http://science.nature.nps.gov/im/units/glkn/index.cfm

Marsh-McBirney. 1990. FLO-MATE Model 2000 portable water flow meter: installation and 

instruction manual. Frederick (MD): Marsh-McBirney, Inc. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 32

NAPAP (National Acid Precipitation Assessment Program). 1990. Acid Deposition: State of 

Science and Technology, Volume II Aquatic processes and Effects. National Acid 

Precipitation Assessment Program Office of the Director, Washington, DC. 

O’Ney, S. E. 2005. Standard operating procedure #5: Procedure for collection of required field 

parameters, Version 1.0. in Regulatory water quality monitoring protocol, Version 1.0, 

Appendix E. Bozeman (MT): National Park Service, Greater Yellowstone Network. 

Penoyer, P. 2003. Vital signs long-term aquatic monitoring projects: Part C, draft guidance on 

WRD required and other field parameter measurements, general monitoring methods 

and some design considerations in preparation of a detailed study plan. Aug. 6, 2003. 

Draft. Available from: http://science.nature.nps.gov/im/monitor/protocols/wqPartC.doc 

Route, B. 2004. Process and results of choosing and prioritizing Vital Signs for the Great Lakes 

Inventory and Monitoring Network. National Park Service, Great Lakes Inventory and 

Monitoring Network. GLKN/2004/05. 

Route, B., W. Bowerman, and K. Kozie. in preparation. Protocol for monitoring environmental 

contaminants in bald eagles. Version 1.1. National Park Service, Great Lakes Inventory 

and Monitoring Network. NPS/GLKN/NRR—200x/xxx. National Park Service, Fort 

Collins, Colorado.

USGS (United States Geological Survey). 2005. National field manual for the collection of 

water-quality data: U.S. Geological Survey Techniques of Water-Resources 

Investigations, book 9, chaps. A1-A9, http://pubs.water.usgs.gov/twri9A

Wagner, R. J., H. C. Mattraw, G. F. Ritz, and B. A. Smith. 2000. Guidelines and standard 

procedures for continuous water-quality monitors: site selection, field operation, 

calibration record computation, and reporting. U.S. Geological Survey Water 

Resources Investigations Report 00-4252. 

Woodyer, K. D. 1968. Bankfull frequency in rivers. Journal of Hydrology 6:114-142. 

WOW. 2004. Water on the Web - Monitoring Minnesota lakes on the internet and training 

water science technicians for the future - a national on-line curriculum using 

advanced technologies and real-time Data (http://waterontheweb.org). University of 

Minnesota-Duluth, Duluth, Minnesota. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #6, page 33

Attachments 

• Field Data Sheet 

• Multiprobe Calibration Log 

• Eureka Manta Maintenance Log 

• Multiprobe Calibration/Maintenance Log 

• Flow Measurements 
GREAT LAKES NETWORK - WATER QUALITY MONITORING ______ initials

Date_____________ Start time_________ End time__________

Secchi (m) 1st_________ 2nd _________ Ave.__________ 

UTM/LatLong________________________________ Secchi reading condition: excellent 1 moderate 2 poor 3

NAD_________ Zone*: 15N 16N WP#_________ Transparency Tube (cm) 1st________ 2nd _________ Ave._________

Water color (visual, field) _____________________

Water sample type: I-tube Grab Van Dorn (Other)__________

Van dorn depth (m) _________________

Elevation (MSL, ft or m?)____________ Zmax (m)_________ probe __________(other_______________)

Barometric Pressure (_____in Hg) (25.4mm/in) = _____mm Hg Median Wave Height (m) ______________

Water Level (m)/ Flow (m/s) 1st_______ 2nd ________ Ave. ________

B= Bottom, Q=QA/QC

NOTES:

DO Cal (% sat.) 

Start________________

Finish_______________

Volume Filtered (ml)

Chl a ________________

TSS _________________

Weather Observations - fill in blanks or circle code

Current Past 48 hours

Wind Direction (as °) _________ Wind Condition Code Rainfall & Wind

Air Temp (°C)________ Smoke rises vertically 0 ___________________

Sky Cover Code Smoke drifts, leaves rustle 1

Clear: < 10% 0 Wind felt on face 2 ___________________

Scattered: 10% to 50% 1 Flag extended, leaves move 3

Broken: 51% to 90% 2 Dust, sm. branches move 4 ___________________

Overcast: > 90% 3 Small trees begin to sway 5

Obscure: precip or obstruction 4 Large branches move, wires 6

Fog 5 whistle, umbrellas hard to control

Light Mist 6 Beyond this you shouldn't be out in a boat

Park____________

Location Name_____________ Site Code_____________

Personnel__________________________________

Instrument(s)_________________________Cal Date_______

Model/Model#____________________________________

DO 

(mg/L)

DO (% 

sat)

pH EC 

(μS/cm)

Depth other

(m)

Temp 

(°C)

* UTM 83 zones: 15N = APIS, MISS, SACN, VOYA; 16N = GRPO, INDU, ISRO, PIRO, SLBE rev. 5/2008
Eureka Manta Multiprobe Calibration 

Personnel Date 

Multiprobe 

Eureka 

Manta 

#309050132 

DO Membrane Changed 

 

Date 

Time 

pH Reference 

Electrolyte Changed 

Date

 

 

Calibration 

Standard 

(True 

Value) 

Pre 

Calibration 

Reading 

Calibration 

Reading 

Calibration 

Check 

Preor 

PostField? 

Battery 

Voltage 

Depth 0 

 

SpCond 

(μS/cm) Air (0) 

SpCond 

(μS/cm) 

value 

Lot# 

SpCond 

(μS/cm) 

value 

Lot# 

SpCond 

(μS/cm) 

value 

Lot# 

 

Temperature 

pH 

 7 

Lot# 

pH 

 10 

Lot# 

pH 

 4 

Lot# 

pH 

 

Lot# 

 

Baro Press. 

DO% 

Saturation 

DO (mg/L) 
Eureka Manta Maintenance Log 

Record maintenance performed, date, and person conducting maintenance 

Date & Personnel DO Probe pH probe EC25 probe Temperature 

Depth 

Sensor 

 

 

 

 

 

 

 
MULTIPROBE CALIBRATION/MAINTENANCE LOG 

PRE FIELD CALIBRATION 

Calibration _______ Initials:_________ Sonde ID:________ Date:______ Time: _______Instrument:________ Battery 

Voltage:___________ 

Function Temp. of 

Standard 

Value of 

Standard 

Initial 

Reading 

Calibrated 

to 

Comments 

Specific conductance 

pH calibrated (~7) 

pH secondary standard (4 or 

10) 

Dissolved oxygen 

DATA NEEDED FOR DISSOLVED OXYGEN CALIBRATION 

Altitude (A )=______________feet above msl Barometric pressure _________ inches 

Barometric Pressure (BP) Options Barometric Pressure Formulas 

Barometer Barometric pressure (inches) ________ x 25.4 = BP ________mm 

From local source after correction (CBP) BP _________ mm = CBP _______mm - 2.5 (altitude ____/100) 

Estimated from altitude only BP _________ mm= 760 mm - 2.5 (altitude _____/100) 

For older Hydrolabs: Table DO value______ x ALTCORR______ x BAROCORR ______= DO standard _______ 

POST FIELD CALIBRATION CHECK Post Calibration Initials: Date: Time: Instrument: Battery Voltage: date of original 

calibration ______ 

Function Temp. of 

Standard 

Value of 

Standard 

Initial 

Reading 

Calibrated 

to 

Comments 

Specific conductance 

pH 7 

pH secondary standard (4 or 

10) 

Dissolved oxygen 

Check previous maintenance and use; do the following before calibration: 

Polish conductivity electrodes. Must be polished within the last 

two months or once every 15 field trips 

Date: Name/comments: 

Change pH reference probe solution. Must be renewed within 

last two months or once every 15 field trips. 

Date: Name/comments: 

Inspect DO membrane for nicks or bubbles. Must be changed 

within last six months or once every 15 field trips. 

Date: Name/comments: 

Change battery. Change once a year. Change internal batteries 

for newer generation products according to guidelines in product 

manual. 

Date: Name/comments: 
Flow Measurements 

Flow condition: 

D=dry, L=low, I=intermediate, H=high, F=flood Clarity condition: 

C=clear, M=muddy, O=other Date: ________________ Start time: ______________ End time: 

___________ Name of 

Stream/River:_______________________________________________________________ Location 

Description:_________________________________________________________________ Field 

Personnel: ____________________________________________________________________ Gage 

height (start): __________________________ Gage height (end): ______________________ 

**Record measurement depth for cable suspension only 

LB/RB 

<======= Circle which bank at start and which bank at finish =========> 

60% or 80% depth 20% depth (ft) 

Distance from 

L / R bank 

(circle one) 

Total 

depth 

(ft) 

1-pt 

meas 

√ 

2-pt 

meas 

√ 

Meas 

depth 

(ft) 

Flow 

velocity 

(fps) 

Meas 

depth 

(ft) 

Flow 

velocity 

(fps) 

0.00 0.00 0.00 

0.00 

 

0.0 0.0 

RB/LB 

Method (circle one for each): Type AA meter or Pygmy meter Rod suspension or cable 

suspension Wading access or boat access or bridge access 

 Total flow:

 Flow: _____________ cfs 

Velocity: __________ fps 

Standard Operating Procedure #7: Processing Water 

Samples and Analytical Laboratory Requirements 

Version 1.0 

In Large Rivers Water Quality Monitoring Protocol 

Prepared by 

Suzanne Magdalene and Daniel Engstrom 

St. Croix Watershed Research Station 

16910 152nd. St. North 

Marine on St. Croix, Minnesota 55047 

and 

Joan Elias (contact author) 

National Park Service 

Great Lakes Inventory and Monitoring Network 

2800 Lake Shore Drive East 

Ashland, Wisconsin 54806 

joan_elias@nps.gov 

August 2008 

Suggested citation: Magdalene, S., D.R. Engstrom, and J. Elias. 2008. Standard operating 

procedure #7: Processing water samples and analytical laboratory requirements. in Magdalene, 

S., D.R. Engstrom, and J. Elias. 2008. Large rivers water quality monitoring protocol, Version 

1.0. National Park Service, Great Lakes Network, Ashland, Wisconsin. NPS/GLKN/NRR—

2008/060. National Park Service, Fort Collins, Colorado.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #7, page ii

Contents 

 Page

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

7.0 Introduction..........................................................................................................................1 

7.1 Summary of Analytical Methods.........................................................................................1 

 

7.2 Sample Handling and Processing Procedures......................................................................3 

 7.2.1 Total Chlorophyll-a ....................................................................................................4 

 7.2.2 Total Suspended Solids...............................................................................................5 

 7.2.3 Unfiltered Samples (TN, TP, Alkalinity, Anions) .....................................................6 

 7.2.4 Filtered Samples (NO3+NO2-N, NH4-N, Cations, SiO2, DOC,).................................6 

7.3 Shipping Procedures ............................................................................................................7 

7.4 Quality Assurance/Quality Control......................................................................................7 

7.5 Data and Records Management ..........................................................................................8 

7.6 Literature Cited ....................................................................................................................9 

Attachment A. Example of a Chain of Custody and Analytical Request Form ...........................11 

Attachment B. Example of an Analytical Services Request Form ...............................................12 

 

Tables 

Page 

Table 1. Summary of water quality analysis methods, detection limits, preservation methods, and 

holding times....................................................................................................................................2 

Table 2. Frequency of analyses of water quality variables..............................................................3 

Table 3. Laboratory equipment and supplies list.............................................................................4 

 

 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #7, page iii

Revision History Log 

 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project leader and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log: 

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #7, page iv

Acknowledgements 

Combinations of existing protocols were used to develop this standard operating procedure for 

handling and processing water samples prior to sending them to an analytical laboratory. The 

authors wish to acknowledge these sources (Baker et al. 1997; EPA 2001; Penoyer 2003; WOW 

2004; Hoffman et al. 2005; O’Ney 2005; and USGS 2005) for the guidance they provided. 

Thanks also go to White Water Associates for providing examples of forms for analytical 

requests and chain of custody and to Rich Axler and Elaine Ruzycki for contributing verbiage to 

early drafts of this document. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #7, page 1

7.0 Introduction 

As part of our water quality monitoring program, we will collect water samples for analysis of 

basic water quality variables that may respond to stressors such as runoff, septic system leakage, 

and recreational use. Because neither the GLKN nor the individual park units currently have 

certified laboratories and instrumentation for performing these analyses, water samples will need 

to be processed soon after collection for transport to a suitable laboratory. Processing samples 

includes filtering and preserving subsamples of water and filters according to methods specific to 

the analyte. This standard operating procedure (SOP) provides detailed instructions on the 

handling and processing of water samples prior to analysis by an analytical laboratory. 

We will collect water samples in the field, according to SOP #6, for the analysis of the following 

water quality variables: 

• Nutrients: total phosphorus (TP), total nitrogen (TN), nitrate+nitrite-nitrogen 

(NO3+NO2-N ), and ammonium-nitrogen (NH4-N) 

• Major cations (Mg+2, Ca+2, Na+

, K+) 

• Major anions (SO4

-2 and Cl-

) 

• Alkalinity 

• Total chlorophyll-a 

• Dissolved silica (SiO2) 

• Dissolved organic carbon (DOC) 

• Total suspended solids (TSS) 

Water chemistry will be performed by one or more analytical laboratories that have 

demonstrated the ability to measure analytes at detection levels adequate to meet our needs. 

Preferably, the laboratories will be state- or federally-certified for performing the above water 

chemistry analyses in natural waters, or an academic research laboratory that can demonstrate 

quality assurance and quality control (QA/QC) procedures consistent with SOP #12 and current 

EPA procedures used as the basis for state certification of commercial environmental 

laboratories. The GLKN’s preference is for laboratories to provide clean sample bottles and 

preservatives, where appropriate, as well as chain of custody documentation and sample logging. 

7.1 Summary of Analytical Methods 

Analytical methods, method detection limits, and procedures related to handling samples change 

over time as the science progresses. Table 1 summarizes examples of the variety of methods, 

detection limits, preservation techniques, and holding times for water samples addressed in this 

protocol. Table 2 summarizes the frequency at which water samples will be collected for 

analysis. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #7, page 2

Table 1. Examples of analytical methods, method detection limits (MDLs), containers, and holding times. 

Analyte Analytical 

Note 1 Method # Det. Limit Vol. 

(ml) Filter Preservation 

Sample 

Bottle 

Note 2 

Hold 

Time 

Titrimetry 310.1 EPA-NERL 10 mg/L 4oC 14 days Alkalinity Spec. auto. 310.2 EPA-NERL 10 mg/L 4o

C 14 days 

 Titrimetry NFM USGS-OWQ 0.01 meg/L Note 4 None none 

ICP 3120B APHA 10 ug/L Note 3 pH<2 HNO3 P or G 6 mos 

Titrimetry 215.2 EPA-NERL 0.5 mg/L Note 3 4o Calcium C 6 mos 

FAA I-3152 USGS-NWQL 0.1 mg/L 250 Note 3 pH<2 HNO3 P 180 day 

IC 300.0 EPA-NERL 0.02 mg/L 4oC P or G 28 day 

Colorimetry 325.2 EPA-NERL 1 mg/L 4o Chloride C 28 day 

Titrimetry 4500-Cl APHA 0.15 mg/L 100 4o

C P or G 28 day 

Chlorophyll-a Spect. 10200 APHA 2 ug/L < 1 L Note 4 Freeze filter P 30day 

Spect. 110.2 EPA-NERL 5 Pt units Note 5 4oC G 48 hours Color Vis. Comp. I-1250 USGS-NWQL 1 Pt-co 250 Note 5 4o

C P 30 days 

Spect. 415.3 EPA 0.018 mg/L 125 Note 3 pH<4 H2SO4 G 28 days DOC Spect. 0-1122-92 USGS 0.1 mg/L 4o

C AG 

ICP 3120B APHA 0.3 mg/L Note 3 pH<2 HNO3 P or G 6 mos K FAA 3111B APHA 5 ug/L Note 3 pH<2 HNO3 P or G 6 mos 

ICP 3120B APHA 20 ug/L Note 3 pH<2 HNO3 P or G 6 mos Mg FAA 3111B APHA 0.5 ug/L Note 3 pH<2 HNO3 P or G 6 mos 

ICP 3120B APHA 30 ug/L Note 3 pH<2 HNO3 P or G 6 mos Na FAA 3111B APHA 2 ug/L Note 3 pH<2 HNO3 P or G 6 mos 

Selective elec. 4500-NH3E 0.08 mg/L 4oC/pH2,0oC 24h/28d 

NH4-N Colorimetry 350.2 EPA-NERL 0.08 mg/L pH<4 H2SO4 28 day 

Titrimetry 4500-NH3 APHA 5 mg/L 4o

C/pH2,0oC 24h/28d 

ICP 3120B APHA 20 ug/L Note 3 pH<2 HNO3 P or G 6 mos 

Spect. 4500- SiO2 D APHA 0.04 mg/L Note 3 No, 4o SiO2 C P 28 days 

FIA-Spect. 4500- SiO2 F APHA 0.78 ug/L Note 3 No, 4o

C P 28 days 

TSS Gravimetric I-3765 USGS-NWQL 1 mg/L 250-

500 Note 4 4o

C filter P NA 

IC 4110C APHA 75 ug/L Note 3 pH<4 H2SO4 P or G 

SO4 CIE-UV D6508 ASTM 0.1 mg/L Note 3 pH<4 H2SO4 ASAP 

Spect. 37512 EPA-NERL 0.5 mg/L Note 3 pH<4 H2SO4 P or G 28 days 

Spect. I-2606 USGS-NWQL 0.001 mg/L 125 MgCl 4oC BrownP 30 days 

Alkaline P USGS 2003 0.01 mg/L 120 Note 6 4oC /H2SO4 TP 48 h/30d 

ICP 200.7 EPA-NERL 60 ug/L pH<2 HNO3 P 6 mos 

Alkaline P USGS 2003 0.03 mg/L 120 Note 6 4oC /H2SO4 48 h/30d 

Titrimetry 4500-N 0-100 mg/L 4o TN C AG 7 days 

Combustion 440.0 EPA-NERL 0.1 mg/L Filter 100 day 

Source: National Environmental Methods Inventory website (NEMI 2006) 

This list is not an endorsement of any particular method or laboratory for any particular analyte. Rather it is to be used as a 

reference for the range of analytical methods available for each analyte. There are surface water conditions (pH, turbidity, other 

elements) that make a particular method unsuitable for a particular situation. As GLKN is monitoring surface water, the methods

listed were chosen as representative of the lower range of detection limits. 

Note 1. CIE-UV= capillary ion electrophoresis with UV detection, FAA = flame atomic absorption, FIA = flow injection 

analysis, IC= ion chromatography, ICP = inductively coupled plasma, Spec. auto = spectroscopy with autoanalyzer 

Note 2. P = plastic (polypropylene), G=glass, AG=amber glass 

Note 3. 0.45μm membrane filter. Pre-filter for dissolved portion analysis. 

Note 4. 0.45μm glass fiber filter. 

Note 5. 0.45μm membrane filter or centrifuge is recommended to remove suspended solids that affect color, however some color 

will also be removed. 

Note 6. USGS 2003. Evaluation of Alkaline Persulfate Digestion as an Alternative to Kjeldahl Digestion for Determination of 

Total and Dissolved Nitrogen and Phosphorus in Water By Charles J. Patton and Jennifer R. Kryskalla. U.S. Geological Survey 

Water-Resources Investigations Report 03-4174. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #7, page 3

Table 2. Frequency of analyses of water samples: monthly sampling for nine months, March 

through November, quarterly sampling (April, July, October). 

Water Quality Variables Monitoring Frequency 

Total Phosphorus (TP) Monthly 

Total Nitrogen (TN) Monthly

Nitrate + Nitrite-Nitrogen (NO3+NO2-N) Monthly

Ammonium-Nitrogen (NH4-N) Monthly

Total suspended solids (TSS) Monthly

Alkalinity Quarterly 

Major Anions (SO4-2, Cl-

) Quarterly

Major Cations (Mg+2, Ca+2, Na+, K+) Quarterly

Dissolved silica (SiO2) Quarterly

Dissolved organic carbon (DOC) Quarterly

Total chlorophyll-a Monthly 

7.2 Sample Handling and Processing Procedures 

The following general techniques will be observed throughout the procedures detailed in 7.2.1 

through 7.2.4. 

1. Keep all water samples cool and dark until processing is complete and samples are 

shipped to the analytical laboratory. 

2. Use only new, clean sample bottles supplied by the analytical laboratory. 

3. Rinse filtration equipment with deionized water (DIW) three times between samples. 

4. Avoid touching the inside of sample bottles and filtering apparatus, tips of forceps, and 

filters to prevent contamination of the samples. 

5. When filtering samples in the field, use an enclosed filtering apparatus to minimize 

contamination from airborne sources. 

6. Wear disposable, powderless gloves when working with acids and other preservatives. 

7. Filter samples in the order of anticipated phosphorus concentrations, from low to high. 

After filtering a water sample that is expected to contain high nutrient concentrations, 

rinse the apparatus three times with 0.1N HCl followed by three times with DIW water 

before processing the next sample. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #7, page 4

8. Prepare QA/QC duplicate samples in the same manner as regular samples, using water 

from the same sample collection container. 

9. Rinse all reusable equipment with DIW immediately, before equipment dries. 

10. Ensure all sample bottles are labeled correctly, completely, and legibly. 

11. Check laboratory equipment and supplies list (Table 3) and ensure equipment is clean 

and ready for use and supplies are adequate. 

12. Prepare a temperature check bottle for each anticipated cooler, if recommended by the 

contract analytical laboratory. Use tap water to fill an extra bottle of the same size used 

for one of the analytes and label as “Temperature Check”. Store this check bottle in 

refrigerator with other samples; package and send to the analytical laboratory with the 

other samples. 

Table 3. Laboratory equipment and supplies list. 

Filtration towers and manifold (4.7 mm) plastic 

Vacuum pump with pressure gauge 

Graduated cylinders, plastic 250, 500 and 1000 mL 

Whatman GF/C filters (4.7 cm diameter) 

0.45 μm Millipore membrane filters (4.7 cm diameter) 

Filter forceps with broad tips 

Aluminum foil 

Labeling tape, permanent markers 

Deionized water (ASTM grade 1 or 2; 1-10 megohm) 

Acid for preservation (according to contract laboratory specifications) 

Freezer and refrigerator 

Plastic storage bags 

Sample bottles (provided by analytical laboratory) 

Insulated ice chest, ice, and ice packs 

Saturated MgCO3 solution (for chlorophyll a), if required by laboratory method 

Adjustable automatic pipettes: 1-5 mL ; 0.2-1 mL; 0.02 -0.1 mL 

Parafin paper roll 

Wash (squirt) bottles – 500 mL 

Kim wipes 

The following sections detail the procedures to be followed when processing water samples for 

particular analysis. 

7.2.1 Total Chlorophyll-a

1. Fit rinsed filtering device with a Whatman GF/C glass fiber filter using forceps, smooth 

side down (curl is up). 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #7, page 5

2. Agitate water sample (always shake well to minimize subsampling error for solids). 

3. Set pump vacuum to < 0.5 atmospheres (7.5 PSI or 380 mm Hg). If using a hand pump, 

maintain pressure at or below 10 PSI. 

4. Use a glass or plastic graduated cylinder to measure 100 - 2500 mLs of water sample. 

Filter sample. If water is very turbid, filter small aliquots (100 mLs) to avoid clogging the 

filter. Sufficient volume has been filtered when a green, brown, or tan color is clearly 

visible on the filter and the flow decreases to a few drops/second. 

5. Add 0.15mls (~3 drops) of saturated MgCO3 during the last 30 mLs of filtering to buffer 

the filter, if required by the method used by the contract analytical laboratory. 

6. Rinse graduated cylinder and filtering apparatus with DIW and pass through filter to 

include any algae that may have adhered to the sides of the cylinder. 

7. Record volume filtered on data sheet (excluding DIW rinse). 

8. Fold filter into quarters with sample on the inside; do not touch filter with fingers. 

9. Wrap filter in foil; label foil with sample location, date and time sample was collected, 

and volume filtered. Place foil in small, sealable baggie with standard laboratory label. 

10. Refrigerate immediately and freeze as soon as possible. Place small baggies with foils 

together in a large, sealable freezer bag. The large freezer bag may be placed in a 

watertight container for shipping to ensure that melt water in transport will not corrupt 

the samples. 

7.2.2 Total Suspended Solids 

1. Use forceps to fit rinsed filtering device with a pre-weighed glass fiber filter supplied by 

the contract analytical laboratory. 

2. Agitate water sample (always shake well to minimize subsampling error for solids). 

3. Use a glass or plastic graduated cylinder to measure 100 - 2500 mLs of water sample. 

Filter sample. If water is very turbid, filter small aliquots (100 mLs) to avoid clogging the 

filter. Sufficient volume has been filtered when the flow decreases to a few drops/second. 

4. Rinse graduated cylinder and filtering apparatus with DIW and pass through filter to 

include any sediment that may have adhered to the sides of the cylinder. 

5. Record volume filtered on data sheet (excluding DIW rinse). 

6. Place filter into container supplied by laboratory; do not touch filter with fingers. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #7, page 6

7. Label container with sample location, date and time sample was collected, and volume 

filtered. 

8. Refrigerate immediately and freeze as soon as possible. Place small baggies together in a 

large, sealable freezer bag. The large freezer bag may be placed in a watertight container 

for shipping to ensure that melt water in transport will not corrupt the samples. 

7.2.3 Unfiltered (Raw) Samples (TP, TN, Alkalinity, Anions) 

1. Rinse sample bottle provided by contract analytical laboratory 1x with sample water 

2. Fill sample bottle with sample water (fill to neck if sample will be frozen) 

3. Refrigerate or freeze, as per laboratory instructions, until packaging for transport to 

analytical laboratory 

7.2.4 Filtered Samples: (NO3+NO2-N, NH4-N, Cations, SiO2 , DOC) 

1. Using clean forceps, place a 0.45μm Millipore cellulose membrane filter in the filtration 

apparatus. Rinse with 100 mL DIW into a cleaned (0.1N HCl and DIW rinsed as per 

sample bottle cleaning) filtering flask (glass or plastic). Rinse flask with filtrate and 

discard filtrate. 

2. Filter a small amount (~50 ml) of sample water; rinse filtering flask with filtrate and 

discard filtrate. 

3. Filter enough of the sample to produce the required amount of filtrate to be tested. 

4. Dispense the filtrate into separate bottles provided by the analytical laboratory as follows: 

• dissolved nutrients - rinse bottle with small amount of filtrate (~10 ml) and discard; 

fill bottle to neck, refrigerate or freeze as per laboratory instructions. 

• major cations - if pre-loaded with HNO3 preservative by the analytical laboratory, fill 

bottle and store at room temperature or refrigerate. If bottle does not come pre-loaded 

with preservative, rinse bottle with small of amount of filtrate (~10 ml) and discard, 

fill bottle approximately 3⁄4 full, add the HNO3 preservative (ampule provided by 

laboratory) and continue to fill bottle until full. Gently roll bottle to mix. Store at 

room temperature or refrigerate. 

• DOC - if pre-loaded with H2SO4 preservative, fill bottle. If bottle does not come preloaded with preservative, rinse bottle with small of amount of filtrate (~10 ml) and 

discard, fill bottle approximately 3⁄4 full, add the H2SO4 preservative (ampule 

provided by laboratory) and continue to fill bottle until full. Gently roll bottle to mix. 

Store at room temperature or refrigerate. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #7, page 7

• Silica – rinse bottle with small of amount of filtrate (~10 ml) and discard, fill bottle 

and refrigerate. 

7.3 Shipping Procedures 

1. Call FedEx or other courier service ahead of time to arrange pick-up. In some cases, 

samples can be sent via bus. 

2. Make large quantities of ice cubes and ice blocks (or buy ice) and freeze gel paks ahead 

of time. 

3. Line cooler with large plastic garbage bag. 

4. Place all total chlorophyll-a baggies containing aluminum foil wrappers in one large 

sealable plastic bag. Place this bag in another sealable bag or in a sealed plastic jar 

between 2 ice packs or bags of ice. It is critical that melt water does not soak the filters. 

5. Repeat step 4 for the total suspended solids filters. 

6. Use ice cubes, in plastic bags, to pack around samples; use other ice blocks (water 

bottles, soda bottles, etc.) as they will fit. 

7. Include a temperature check bottle in each cooler with the sample bottles, if used by the 

contract analytical laboratory. 

8. Complete the chain of custody (COC) form, keeping the ‘client copy’ for the project files. 

Seal the laboratory’s copies in a one-gallon plastic sealable bag and tape to the inside 

cover of the cooler. Prepare separate COC forms for each cooler. An example COC form 

is provided in Attachment A. 

9. If the refrigerated samples are sent in the same insulated cooler with the frozen samples, 

protect them from freezing by wrapping them in newspaper, bubble wrap, etc. 

10. Ship samples overnight so they are received the following day during a work-week, 

whenever possible. Contact the laboratory about Saturday shipment receipt availability 

before shipping samples on a Friday. Many laboratories do not have sample receipt staff 

on Saturday or charge extra for staff time. 

11. Alert the contract laboratory when samples have been shipped and provide them with the 

tracking number. 

7.4 Quality Assurance/Quality Control 

Quality assurance/quality control refers to all those things good investigators do to ensure their 

measurements are accurate (the absolute true value) and precise (reproducible, consistent), and 

that they include a good estimate of their uncertainty. It specifically involves following 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #7, page 8

established rules in the field and laboratory to assure everyone that the sample is representative 

of the site, free from outside contamination, and that it has been analyzed following standard 

QA/QC methods. These methods typically involve comparing the sample to a set of known 

samples for estimating accuracy and replicating the measurement to estimate its precision. 

In the context of field sampling and processing, quality assurance protocols are meant to ensure 

that data collected are as representative of the lake or stream site as possible. Such procedures 

include implementing good field procedures and quality-control checks, careful post-collection 

processing of water samples to minimize artifacts due to contamination or mis-labeling, proper 

storage and preservation techniques while in transit to a laboratory, and proper QA/QC by the 

laboratory itself. See SOP # 12, Quality Assurance/Quality Control, for more details. 

Quality assurance at the batch level (within the laboratory) is accomplished by using proper 

techniques and replicating 10% of the field samples. 

The most important aspects of quality control in the collection of water quality samples are: 1) 

Samples collected should represent the river at the time the samples are collected, such that the 

samples produce the quality of information necessary to meet the objectives of the project; and 

2) the integrity of the samples collected is not compromised by contamination, misidentification, 

or improper sample handling or preservation. 

To help meet these quality control aspects, the transport and tracking of the samples from the 

field to the analytical laboratory that performs the chemistry analyses is critical. Each set of 

samples should include an Analytical Services Request (ASR) form supplied by the laboratory 

(see Attachment B for an example), which accompanies a Chain of Custody Form. To ensure 

correct processing of samples, the information recorded on the ASR form must correspond to 

each sample in the shipment. Check with individual analytical laboratory requirements for 

correct labeling codes and procedures. At the bottom of the ASR form, list the total number of 

sample bottles for each sample-designation code. To prevent water damage to paperwork 

accompanying samples to the laboratory (such as the ASR form and the Chain of Custody form), 

place all paperwork inside a sealable plastic bag and tape the bag to the underside of the cooler 

lid. Keep a copy of the completed ASR and COC forms in the project files and a backup copy 

offsite. 

7.5 Data and Records Management 

Complete and accurate record keeping of field-derived data is an essential component of 

monitoring water quality. Field technicians, crew leaders, and project leaders share responsibility 

for collecting, verifying, and documenting data according to the guidelines in this monitoring 

protocol and all applicable standard operating procedures. Data and records management include 

the following responsibilities: 

1. Refer to the GLKN Data Management Plan (Hart and Gafvert 2005) for overall guidance. 

2. Follow the QA/QC procedures in SOP #8 for specific instructions on data entry, 

management, verification, and validation. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #7, page 9

3. Record and verify observed or measured data values, including completing paper forms 

and entering data into NPSTORET and/or other electronic databases. NPSTORET 

maintains the necessary relationships between data values, equipment configuration and 

calibration, procedures, methods, and metadata. 

4. Schedule and perform regular data transfer and backup. Data will be protected from loss 

or damage by daily backup when possible, or on a feasible schedule approved by the 

project leader and the data manager. 

5. Review, verify, and correct field data and sample processing information as soon as 

possible after the actual sampling (see SOP #8 for more details). 

6. Prepare data and procedural documentation, especially deviations from the protocol or 

study plan, including metadata forms in NPSTORET and additional documentation 

requested by the project manager or data manager. 

7. Ensure that field forms, field notebooks, and other hardcopy records are secure, 

organized, and available for viewing, reproduction, or transfer upon request. 

7.6 Literature Cited 

Baker, J. R., D. V. Peck, and D. W. Sutton (editors). 1997. Environmental Monitoring and 

Assessment Program Surface Waters: Field Operations Manual for Lakes. EPA/620/R97/001. U.S. Environmental Protection Agency, Washington D.C. 

http://www.epa.gov/emap/html/pubs/docs/groupdocs/surfwatr/field/97fopsman.html 

EPA (US Environmental Protection Agency). 2001. Guidance for preparing standard operating 

procedures (SOPs): EPA QA/G-6. Washington (DC): U.S. Environmental Protection 

Agency. Report nr EPA/240/B-01/004. 58 p. Available from: 

http://www.epa.gov/quality/qs-docs/g6-final.pdf

Hart, M., and U. Gafvert. 2005. Data management plan: Great Lakes Inventory & Monitoring 

Network (draft). National Park Service Great Lakes Inventory and Monitoring Network 

GLKN/2005/20. 

Hoffman, R. L., T. J. Tyler, G. L. Larson, M. J. Adams, W. Wente, and S. Galvan. 2005. 

Sampling protocol for monitoring abiotic and biotic characteristics of mountain ponds 

and lakes. Chapter 2 of Book 2, Collection of Environmental Data, Section A, Water 

Analysis Techniques and Methods 2-A2. U.S. Department of the Interior, U.S. 

Geological Survey, Reston, Virginia. 

NEMI. 2006. National Environmental Methods Index website as accessed during the 

 month of July, 2006. http://www.nemi.gov 

O’Ney, S. E. 2005. Standard operating procedure #5: Procedure for collection of required field 

parameters, Version 1.0. in Regulatory water quality monitoring protocol, Version 1.0, 

Appendix E. Bozeman (MT): National Park Service, Greater Yellowstone Network. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #7, page 10

Penoyer, P. (National Park Service Water Resources Division). 2003. Part C: Vital signs longterm aquatic monitoring projects, draft guidance on WRD required and other field 

parameter measurements, general monitoring methods and some design considerations in 

preparation of a detailed study plan, 2003 Aug 6 Draft. Available from: 

http://science.nature.nps.gov/im/monitor/protocols/wqPartC.doc

USGS (US Geological Survey). 2003. Evaluation of alkaline persulfate digestion as an 

alternative to Kjeldahl digestion for determination of total and dissolved nitrogen and 

phosphorus in water, by Charles J. Patton and Jennifer R. Kryskalla. U.S. Geological 

Survey Water-Resources Investigations Report 03-4174. 

USGS (US Geological Survey). 2005. National field manual for the collection of water-quality 

data: U.S. Geological Survey Techniques of Water-Resources Investigations, book 9, 

chaps. A1-A9, http://pubs.water.usgs.gov/twri9A. 

WOW. 2004. Water on the Web - Monitoring Minnesota Lakes on the Internet and Training 

Water Science Technicians for the Future - A National On-line Curriculum using 

Advanced Technologies and Real-Time Data.(http://waterontheweb.org). University of 

Minnesota-Duluth, Duluth, Minnesota 55812. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 

SOP #7, page 11

Attachment A. Example of a chain of custody and analysis request form
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #7, page 12

Attachment B. Example of an analytical services request 

form 
Standard Operating Procedure #8: 

Data Entry and Management 

Version 1.0 

In Large Rivers Water Quality Monitoring Protocol 

Prepared by 

Joan Elias and Mark Hart 

National Park Service 

Great Lakes Inventory and Monitoring Network 

2800 Lake Shore Drive East 

Ashland, Wisconsin 54806 

joan_elias@nps.gov 

August 2008 

Suggested citation: Elias, J., and M. Hart. 2008. Standard operating procedure #8: Data entry 

and management. in Magdalene S., D. R. Engstrom, and J. Elias. 2008. Large rivers water 

quality monitoring protocol, Version 1.0. National Park Service, Great Lakes Network, Ashland, 

Wisconsin. NPS/GLKN/NRR—2008/060. National Park Service, Fort Collins, Colorado.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #8, page ii 

Contents 

 Page

Revision History Log.................................................................................................................... iii 

Acknowledgements....................................................................................................................... iv 

8.0 Introduction.........................................................................................................................1 

8.1 Data Stewardship Roles and Responsibilities.....................................................................1 

 

8.2 NPSTORET Database.........................................................................................................1

 8.2.1 Database Design.........................................................................................................3 

 

8.3 Data Management Procedures ............................................................................................3 

 8.3.1 Data Collection ..........................................................................................................3 

 8.3.2 Data Entry, Verification, and Documentation ...........................................................4 

 8.3.3 Data Validation ..........................................................................................................6 

 8.3.4 Data Analysis and Reporting .....................................................................................6 

 8.3.5 Data Folder and File Organization.............................................................................7 

 8.3.6 Data Archival and Distribution Procedures ...............................................................7 

 

8.4 Literature Cited ...................................................................................................................9 

 

Tables 

 Page 

Table 1. Data stewardship responsibilities of water quality monitoring personnel.........................2 

Figures 

 Page 

Figure 1. Schematic of data flow .....................................................................................................3 

Figure 2. Great Lakes Network folder structure ..............................................................................8 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #8, page iii 

Revision History Log 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project manager must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the header of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log: 

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #8, page iv 

Acknowledgements 

Primarily, we relied on the Great Lakes Network’s data management plan (Hart and Gafvert 

2005) in writing this document. Standard operating procedures for the entry and management of 

data written by other networks also provided guidance.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #8, page 1

8.0 Introduction

Water quality data collected under the large rivers water quality monitoring protocol (Magdalene 

et al. 2008) must be entered, quality-checked, documented, managed, and made available to 

others for a variety of purposes, such as management decision-making, research, and education. 

The National Park Service (NPS) Water Resources Division (WRD) developed a database 

application called the Water Quality Database Template, or NPSTORET, to facilitate 

management of water quality data. NPSTORET allows importing of water quality data into the 

National STORET (STOrage and RETrieval) Data Warehouse administered by EPA, as required 

by the water quality component of the Natural Resource Challenge (NPS 1999). 

This standard operating procedure outlines data stewardship responsibilities and provides 

specific instructions and references for entering, quality checking, and managing water quality 

data. 

8.1 Data Stewardship Roles and Responsibilities

The purpose of data stewardship is to share the responsibility for managing data and information 

resources that are organized, useful, compliant, available, and safe. The demand for detailed, 

high quality data and information about water quality requires a group of people working 

together to ensure that data are collected using appropriate methods, and that resulting datasets, 

reports, maps, and other derived products are well-managed. 

The Great Lakes Network (GLKN) aquatic ecologist serves as project manager for water quality 

monitoring. The project manager will supervise data collection, provide project oversight, direct 

on-the-ground data collections, and provide cohesive links among data collection, synthesis, 

interpretation, and reporting. 

While the project manager must act as the steward for water quality monitoring data for the 

Network, other project and GLKN personnel are also accountable for specific data management 

tasks. Table 1 lists stewardship responsibilities of personnel involved in the management of 

water quality data. To ensure that all project data are managed properly, individuals must 

understand their responsibilities, communicate with one another, and assist one another as 

needed. 

8.2 NPSTORET Database 

Water quality data are managed according to guidelines from the NPS Water Resources 

Division. In accordance with these guidelines, the desktop database application NPSTORET, 

also known as Water Quality Database Templates, will be used to enter, store, document, and 

transfer water quality data. The GLKN oversees the use of NPSTORET per the Network’s water 

quality monitoring protocols and ensures that data are transferred at least annually to the NPS 

Water Resource Division for upload to the STORET database (Figure 1). 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #8, page 2

STORET is an interagency water quality database developed and supported by the 

Environmental Protection Agency (EPA) to house local, state, and federal water quality data 

collected in support of managing the nation’s water resources under the Clean Water Act. NPS 

Director’s Order 77 indicates that the NPS should archive water quality data in STORET, and the 

NPS WRD mandates that any data collected as part of a WRD-funded project get archived in 

STORET. The NPS uses STORET as a repository of physical, chemical, biological, and other 

monitoring data collected in and around national park units by park staff, contractors, and 

cooperators. The NPS operates its own Service-wide copy of STORET and makes periodic 

uploads to the EPA STORET National Data Warehouse so that data collected by and for parks 

will be accessible to the public. 

Table 1. Data stewardship responsibilities of water quality monitoring personnel. 

Personnel Role Data Management Responsibilities Related to Water Quality Monitoring 

Project Crew 

Member 

Crew members collect and manage data with direction and guidance from the crew 

leader and/or project manager. Data collection includes calibrating and operating 

sampling equipment, collecting water samples, and recording measurements and 

observations. Crew members are responsible for quality control by following data 

collection and recording instructions and by promptly verifying recorded data. Crew 

members may also perform data entry and verification. 

Project Crew 

Leader 

The crew leader normally performs the same duties as the other crew members and 

ensures adherence to data collection and processing protocols, including data 

verification and documentation. The crew leader also works with the project 

manager and data manager on water quality data management in the office. 

Project Manager 

(Network 

Aquatic 

Ecologist) 

The project manager is responsible for all project operations and results, and may 

also participate in field operations. The project manager ensures that data 

management activities are conducted according to established procedures and is 

responsible for data validation: approving the data content, quality, and 

documentation, as well as making decisions about data sensitivity and distribution. 

The project manager is responsible for evaluating project data at specified intervals, 

analyzing data for trends, and following reporting requirements. 

Resource 

Specialist 

The water resource specialist, who may also serve as a crew leader, works closely 

with the project manager in all aspects of data management. The water resource 

specialist collects field data, enters field and laboratory data, verifies data, and 

validates data. 

Network Data 

Manager 

The network data manager, together with the project manager, ensures that water 

quality monitoring data are organized, useful, compliant, available, and safe. The 

network data manager provides the most current version of NPSTORET and works 

with project personnel to ensure Network water quality data are received by WRD. 

The network data manager oversees activities related to training, user support, 

quality assurance, documentation, backups, archiving, and data maintenance and 

distribution. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #8, page 3

Figure 1. Schematic of data flow: water quality data are transferred from the Network to the 

national service-wide database and ultimately to EPA’s master database. Public access to 

STORET is available via an on-line clearinghouse. 

8.2.1 Database Design 

The database design for NPSTORET is described in its associated documentation. Because it 

must be compatible with the Oracle-based EPA STORET, NPSTORET is a complex MS Access 

implementation. The latest version of NPSTORET can be found at: 

http://nrdata.nps.gov/programs/water/npstoret/

GLKN has a number of different avenues for data distribution depending on the audience served 

and the degree of analysis and customization needed by the end-user (see GLKN’s data 

management plan, Hart and Gafvert [2005], for more details). One of the primary methods 

GLKN uses for data distribution is the Vital Signs Internet Mapping Service (VSIMS) that 

allows users to explore and query monitoring data using spatial and non-spatial parameters. 

Network (GLKN) versions of NPSTORET are used to update a master version of STORET 

maintained by NPS WRD. The WRD master copy of STORET data is the data source that is 

used by the VSIMS to serve water quality data collected by GLKN and other I&M networks. 

The Great Lakes Network will maintain one master copy of NPSTORET for each park at the 

Ashland office on a central server. This is the only copy of NPSTORET that can be used to 

export data to other locations (i.e., WRD and GLKN’s SQL Server). Additional copies of 

NPSTORET can be used by GLKN personnel stationed at parks, but they can only be used as a 

conduit for data entry and the importation of data to GLKN’s master version of NPSTORET. For 

analysis, the data from the master copy of NPSTORET, that has passed all QA/QC procedures, 

must be used.

8.3 Data Management Procedures 

8.3.1 Data Collection 

Data values are measured, observed, or estimated according the GLKN large rivers water quality 

monitoring protocol at various monitoring locations (sample sites) and recorded on field forms 

(see SOP #6, Field Measurements and Water Sample Collection). Crew members are responsible 

for legible, accurate entries on field forms and in log books, including the calibration log. As a 

first step to verify data, crew members will check and double-check the recorded values on the 

day of data collection. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #8, page 4

Data collected with a multiparameter sonde are stored directly on a datalogger attached to the 

sonde and recorded on the field sheets at the time of sampling. The hard copy of the data serves 

as a back-up should something happen to the electronic data. 

Digital images of sample sites are acquired during site establishment (SOP #4) and periodically 

as sites change (SOP #6). Crew members are responsible for proper settings and use of digital 

camera equipment and should refer to the user manual for details specific to the camera. 

GPS coordinates are stored as waypoints if using a recreational GPS unit, or as features if using a 

mapping-grade unit with a data dictionary, and recorded on the field sheets. When possible, the 

GPS data will be differentially corrected to improve the accuracy of location coordinates. See 

SOP #3 for more information on using a GPS unit. 

Water samples are collected, labeled, and packaged for laboratory analysis according to SOPs #6 

and #7. Identification numbers on sample containers, chain of custody forms, laboratory reports, 

and on the field data collection form facilitate management of laboratory results. 

8.3.2 Data Entry, Verification, and Documentation 

Requirements for data entry into NPSTORET are detailed in the documentation for users. We 

present a summary of data entry below, and refer staff to the most recent NPSTORET 

documentation for the specifics. 

On a regular schedule approved by the project manager and data manager, the crew leader 

gathers the field data collection forms and verifies the completeness, accuracy, and legibility of 

each form. Following each round of sampling, the crew leader will make a photocopy of each 

field form and ensure each copy is legible; one copy will be placed in the site binder kept at the 

park, and the original will be archived in the GLKN office. Upon receiving the data sheets, the 

project manager will proofread them, making sure that they have been filled out completely. All 

data sheets should have been reviewed for completeness while in the field, however some 

deficiencies in data recording may not be identified until all data sheets have been reviewed as a 

group. 

Electronic data from the multiparameter sonde are downloaded from the datalogger to a 

computer in an MS Excel spreadsheet or text file at the end of each sampling day or as soon as 

feasible after sampling, and verified for accuracy. Likewise, at the end of each sampling day or 

as soon as feasible after sampling, all digital images will be downloaded to a computer and 

labeled with date, location, and subject matter. Both of these types of electronic data will then be 

imported into NPSTORET. 

Project staff enters site establishment data in the NPSTORET Station Entry Template as soon as 

possible following the initial site visit to each sample location. This prompt action is a good data 

management practice and an NPSTORET requirement that enables parameter data entry. Linking 

digital images of sample sites to stations in NPSTORET is required as part of this data entry 

process.

File size for digital images linked to stations in NPSTORET should normally be at least 100kb 

and less than 300kb. Project staff will reduce the size of image files larger than 300kb and copy 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #8, page 5

images to a file folder named “images” for the appropriate park. Original ‘raw’ images can be 

stored in the Images folder (see Folder and File Organization below) if project staff determine it 

is important to keep higher resolution images. 

Import data from the MS Excel spreadsheet into NPSTORET following the guidelines. Any 

notes taken in the field regarding collection of data with the sonde are transcribed to NPSTORET 

in a field for comments and notes. 

Results of laboratory analyses typically are sent to the project manager in a MS Excel 

spreadsheet and on hard copy forms. The project manager will verify both sets of data and 

follow-up with the contract laboratory if any discrepancies are noted or any questionable results 

are reported (see SOP #12 on QA/QC for more details). Project staff will import the verified data 

into NPSTORET. 

On a regular schedule approved by the project leader and data manager, project staff will enter 

the verified field data from both hard copy and data logger in NPSTORET. Several times each 

season the project leader will perform or coordinate a random spot check of ten percent of the 

characteristic values entered in NPSTORET that season. The project leader resolves errors 

according to established procedures. See SOP #12 for additional QA/QC details.

Data verification starts with the QA/QC steps that are detailed in SOP #12. As data are entered 

into NPSTORET, either by keyboard or using an import routine, a suite of QA/QC procedures 

exist that compare the entered data with expected formats and accepted data value ranges or 

domains. If the entered data do not pass a form-based QA/QC test, NPSTORET prompts the user 

to make corrections and re-enter the data. For most of the form-based tests, the NPSTORET 

database will not accept out-of-bounds data, and correction is mandatory; for some range tests, 

out-of bounds data are accepted after a user prompt, but are flagged accordingly. The QA/QC 

procedures on imported data perform similar tests, but exceptions that do not pass QA/QC are 

presented to the user and must be reconciled before the record or dataset can be accepted by 

NPSTORET. 

Additional comparison tests will be run on data in NPSTORET to flag records that are outside 

the expected rate of change for a parameter based on previous records for that parameter. These 

suspect data points are reviewed by an expert user and can be corrected, flagged, or excluded 

from the dataset. 

As mentioned above, NPSTORET performs numerous QA/QC checks on the data as they are 

entered and stored. Additionally, once the data are transferred to WRD, more QA/QC procedures 

are performed. The Network’s water quality data records are regarded as being in provisional 

status until they are returned to GLKN from WRD, or are accepted by WRD without changes 

after the final QA/QC steps. Each individual record in the water quality dataset always has one, 

and only one, status flag indicating its status as provisional or final. Finalized data can still be 

edited and changed if errors are discovered after review in reporting and analysis, but the status 

of those records reverts to provisional and they must be resubmitted to the master STORET 

version at WRD and returned before they can be reassigned as finalized data records. 

A user’s identification is assigned to each aspect of data handling, from collection through the 

final steps of QA/QC. On data sheets, the identity of the data collector(s) is recorded and is 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #8, page 6

transcribed into the data entry forms in NPSTORET. Additionally, NPSTORET records the user 

name (login) for every table entry or modification. Only qualified users who have been trained 

and given edit permissions are allowed to edit data in NPSTORET. These procedures protect the 

integrity of the data and allow the history of each data record to be traced. 

Executive Order 12906, mandates federal agencies to “...document all new geospatial 

data it collects or produces, either directly or indirectly...” using the Federal Geographic 

Data Committee Content Standard for Digital Geospatial Metadata. Water quality monitoring 

meets the definition of geospatial data and, thus, GLKN is responsible for documenting all public 

datasets using metadata that meets that standard. NPSTORET requires and stores a great deal of 

metadata at the record and project level. Metadata will be developed to meet the federal standard, 

using NPSTORET as a primary source. Consult the GLKN Data Management plan (Hart and 

Gafvert 2005) for additional details about metadata procedures and requirements.

8.3.3 Data Validation

Prior to distributing the data for any type of use, the project manager or other appropriate water 

resource specialist validates the NPSTORET database content in the master water quality data 

file according to procedures in the Quality Control and Quality Assurance SOP. The integrity of 

each master data file must be preserved during the validation process in cases where the person 

performing data validation does not have direct access to the master water quality data file. 

Validation is performed at least once each year after data collection and entry are complete and 

before data are submitted to the NPS Water Resource Division, usually by the end of each 

calendar year. If this annual validation does not meet scheduled reporting requirements of the 

Network, then the project manager may coordinate more frequent validation to meet needs, or 

reports can include a statement explaining that results are based on data that have not been 

validated. The statement should include an explanation of what significance this has for using 

preliminary data. 

Laboratory results must be entered and validated in NPSTORET as soon as possible following 

receipt of the results. The project manager coordinates receiving and entering data with project 

staff and then performs or coordinates the validation of lab results. 

8.3.4 Data Analysis and Reporting 

Project staff will follow the procedures for data analysis in SOP #9 and data reporting in SOP 

#10. Data summary statistics will typically include, but not be limited to: 

• Mean 

• Median 

• Standard deviation 

• Minimum 

• Maximum 

• Count 

• Percentiles (10, 25, 75, and 90th percentiles) 

• Standard error 

• Variance 

• Range 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #8, page 7

• Mode 

• Sum 

• Kurtosis 

• Skew 

Some of these statistics are available through NPSTORET’s query function and others can be 

derived from NPSTORET outputs. NPSTORET provides an export for any portion of the data in 

tabular format for use with the Data Analysis Toolpak. 

8.3.5 Data Folder and File Organization 

All data from this water quality protocol should be stored, at the earliest possibility, on the 

GLKN central server. A diagram of the folder structure is shown below (Figure 2). 

Files should be named in accordance with the file-naming standards in the GLKN Data 

Management plan (see section 6.4 of Hart and Gafvert 2005). Files have a ‘GLKN’ prefix, a 

descriptive element, and finish with a date element. For example, GLKN_ 

ISRO_Field_Data_20070605.doc contains field data from Isle Royale National Park on June 5, 

2007. Do not use spaces in file names. 

8.3.6 Data Archival and Distribution Procedures 

Data archiving serves two primary functions: it provides a source to retrieve a copy of any data 

set when the primary dataset is lost or destroyed, and it provides a data record that is an essential 

part of the QA/QC process. Original data will be archived at the Network office. Original data 

for printed forms are either the physical data sheets or exact and complete digital copies of the 

forms that capture all entries and notations. The unedited files are the original data for digital 

data. 

All digital data have a duplicate file created at the earliest opportunity. At least two complete 

copies of any water quality dataset are required by WRD, including digital replicas (scanned 

versions), if they are created, of hard copy data sheets. Digital field data that are entered directly 

into a field computer or collected from a data logger must be backed up to a second medium at 

the earliest possibility. The data files on field computers and loggers must not be erased until the 

integrity of these data files are verified on the duplicate storage medium. The removal of original 

data files from a field computer or logger must be a balance of keeping memory available for 

new data collection and a need to keep data in their most original form for as long as possible. 

Field files should only be deleted when memory space is needed for new data collection. 

The Network’s master version of NPSTORET is maintained on a central server in the Ashland 

Office that is backed up daily, and backed up off-site weekly. Complete details of the GLKN 

Server archiving procedure are found the Infrastructure chapter of GLKN’s Data Management 

Plan (Hart and Gafvert 2005); the general strategy for data archiving is also described in this plan 

and its appendices. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #8, page 8

Figure 2. Great Lakes Network folder structure for information related to the protocol for 

monitoring water quality in large rivers. Data are organized in subfolders by year within each park 

folder. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #8, page 9

Public distribution, as well as long-term archival of water quality data, is provided by the NPS 

WRD STORET database and the National EPA STORET Data Warehouse and their associated 

online interfaces. As stated above, the Network will send its master version of NPSTORET to 

WRD at least annually. In cases where more recent data are requested, the project manager or 

appropriate water resource specialist will respond based on the nature of each request and the 

state of the data, for example, whether or not the data are fully qualified and documented to meet 

the needs of the requestor. 

8.4 Literature Cited

Hart, M., and U. Gafvert. 2005. Data management plan: Great Lakes Inventory & Monitoring 

Network (draft). National Park Service Great Lakes Inventory and Monitoring Network 

GLKN/2005/20. 

Magdalene, S., D. R. Engstrom, and J. Elias. 2008. Large rivers water quality monitoring 

protocol, Version 1.0. National Park Service, Great Lakes Network, Ashland, Wisconsin. 

NPS/GLKN/NRR—2008/060. National Park Service, Fort Collins, Colorado.

NPS (National Park Service). 1999. Natural Resource Challenge. Available from: 

<http://www.nature.nps.gov/challenge/index.cfm>. Accessed January 26, 2007. 

Standard Operating Procedure #9: 

Data Analysis 

Version 1.0 

In Large Rivers Water Quality Monitoring Protocol 

Prepared by 

Suzanne Magdalene and Daniel Engstrom 

St. Croix Watershed Research Station 

16910 152nd. St. North 

Marine on St. Croix, Minnesota 55047 

and 

Joan Elias (contact author) 

National Park Service 

Great Lakes Inventory and Monitoring Network 

2800 Lake Shore Drive East 

Ashland, Wisconsin 54806 

joan_elias@nps.gov 

August 2008 

Suggested citation: Magdalene S., Engstrom D. R., and Elias J. 2008. Standard operating 

procedure #9: Data analysis. in Magdalene S., D. R. Engstrom, and J. Elias. 2008. Large rivers 

water quality monitoring protocol, Version 1.0. National Park Service, Great Lakes Network, 

Ashland, Wisconsin. NPS/GLKN/NRR—2008/060. National Park Service, Fort Collins, 

Colorado.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #9, page ii

Contents 

 Page

Revision History Log.................................................................................................................... iii 

Acknowledgements....................................................................................................................... iv 

9.0 Introduction.........................................................................................................................1 

9.1 Initial QA/QC Checks for Data Outliers.............................................................................1 

9.2 Adjustment for Flow...........................................................................................................1 

9.3 Spatial Domains of Analysis...............................................................................................2

9.4 Annual Data Summaries .....................................................................................................2

9.5 Long-Term Trend Analyses................................................................................................3 

 9.5.1 Recommended Methods for Long-Term Trend Analysis..........................................3 

 9.5.2 Approaches to Analyze Frequently-Collected Data ..................................................3 

 9.5.3 Duplicate Sampling....................................................................................................4

 9.5.4 Other Analytical Considerations................................................................................4 

9.5 Literature Cited ...................................................................................................................5 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #9, page iii

Revision History Log 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project manager must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the header of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log: 

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #9, page iv

Acknowledgements 

The authors would like to thank Roy Irwin and Erik Beever for their guidance and thoughtprovoking discussions regarding analysis of water-quality data. 

.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #9, page 1

9.0 Introduction 

Data analysis is the process by which observations of the environment are turned into meaningful 

information. This includes all evaluations of data after the data have been collected and entered 

into an electronic file or database and undergone a check of the data entry to ensure quality. Data 

analysis includes quality assurance/quality control (QA/QC) checks for statistical outliers prior 

to data summarization, extending through exploratory data analysis, and concluding with 

analyses that lead to summary and interpretation of the data. 

The appropriate method for analyzing monitoring data is tightly linked to the monitoring 

objectives, the spatial and temporal aspects of the sampling design, and the expected uses of the 

data by managers (MacCluskie et al. 2004). Methods of data analysis need to be considered well 

before the data are even collected. 

As described in the GLKN protocol narrative for monitoring water quality in large rivers 

(Magdalene et al. 2008), the sample design of this protocol includes both targeted and 

probabilistic sampling. In other words, it includes some sites that are selected nonrandomly (e.g., 

monitoring stations that have a long historical legacy) and others that are selected randomly. 

These two types of sites represent independent domains within the population of waterbodies 

that GLKN has defined as ‘large rivers’ within its nine park units. Therefore, each type of site 

will require its own method of data analysis (discussed below). 

9.1 Initial QA/QC Checks for Data Outliers 

All water quality data undergo several quality assurance/quality control (QA/QC) procedures 

(e.g., duplicate sampling, data-entry filters, removal of logically inconsistent entries; see SOP #8 

for data management details) to ensure that the data accurately represent the natural environment 

at the time of sampling. Data points that do not meet limitations for precision or bias may be 

flagged or eliminated from the database. 

Some statistical measures, like population mean, are sensitive to extreme atypical values, or 

outliers. Therefore, to reveal the central tendency of the population, the project manager may 

elect to remove outliers from the data pool. However, such removals should be performed with 

great caution, and usually only when it is clear that the outlier truly did not reflect system 

properties (e.g., due to instrument error, transcriptional error). Outliers may be identified by a 

variety of methods, including scatter plots, box-and-whisker plots, and Grubbs’ test. 

9.2 Adjustment for Flow 

Flow directly influences the values of most water-quality variables; many metrics are expressed 

in units of concentration (i.e., mass per unit volume). The purpose of monitoring water quality is 

often to detect change in the total mass of a variable, independent of volume of water present. 

Ideally, without budget constraints, this mass is directly calculated from continuous records of 

flow and high-frequency water sampling. However, in the face of budget constraints, flowadjustment is another method to account for the effect of flow. Flow-adjusted concentrations are 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #9, page 2

thus not subject to the confounding influence that variable flow rates can produce. In particular, 

one uses regression or a smoothing technique (e.g., LOWESS) to obtain residuals from a 

relationship of concentration vs. flow (on a log-log scale). Trend analysis is subsequently 

performed on the residuals, which are presumably de-trended for flow. The trend in the residuals 

can be back-transformed to yield the trend in concentration units per year. 

9.3 Spatial Domains of Analysis

Whereas some analyses may analyze trend at individual stations only (e.g., to investigate the 

effect of a local, point-source contamination), the most convincing conclusions will usually 

derive from results obtained across a collection of sites. Alternative domains of analysis include 

a portion of a park unit (e.g., the upper St. Croix River), an entire park unit, all monitoring 

stations on GLKN non-wadeable rivers, or regional or national domains. In these cases, 

individual stations constitute replicates, and the variability among stations provides an indication 

of the consistency in values across the larger landscape (within the chosen domain). Analysis of 

trend thus indicates whether a given water-quality parameter is changing or not across an entire 

region. Domains can be constructed to include several different sub-regions of, for example, a 

particular park unit. These sub-regions should be based on dominant physical or ecological 

gradients that are meaningful to the target indicator and not expected to vary through time. Thus, 

to the extent that stratification reduces the CV within parameters of interest, it will increase 

power to detect change over time, if total sample size is kept constant. It should be remembered, 

however, that if sampling units within a given domain are not selected probabilistically (with 

respect to how the domain is specifically defined), extrapolating results to broader domains 

should not be performed. Accordingly, appropriate caveats must be provided for interpretation of 

results provided. 

9.4 Annual Data Summaries 

Brief characterizations of the data from each NPS unit that was sampled and the Network as a 

whole will be performed each year, after all QA/QC procedures have been completed. For each 

station sampled, these descriptive statistics will include mean, median, maximum and minimum 

values, as well as skew, kurtosis, and measures of variability (e.g., coefficient of variation (CV), 

standard error, variance) for each water quality variable. Understanding of landscape-scale 

dynamics will be provided by analyses of variability among stations within the domain of 

interest (for example, the riverine-lake portion of the lower St. Croix River). 

Given the relevant legislation (e.g., Clean Water Act of 1972), it may be of interest to the 

individual NPS units and to other entities to assess the proportion of measurements during a time 

period or across a domain (at a single point in time) that exceed pre-determined thresholds. As 

with nearly all percentage data, arcsine transformations must be performed on those data before 

statistical analyses can be conducted (Sokal and Rohlf 1995). 

Ideally, analyses of variability in selected parameters at the appropriate spatial and temporal 

scales should also occur within the first two to three years of the monitoring program, to ensure 

that the variability in historical data correctly informed our a priori power analyses for 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #9, page 3

determining the minimum number of sites needed to detect specific levels of change with 80% 

power. 

9.5 Long-Term Trend Analyses 

Following collection of at least three years of data at a given park, analyses more detailed than 

the data summaries described above may be conducted. Approaches to such detailed analyses 

may include estimation of interannual change, graphic approaches (e.g., comparison of mean and 

variability in a parameter in the current year versus during past years), and occasionally 

qualitative analysis (Guthery et al. 2001), as well as modeling, correlational analyses, and 

various parametric and nonparametric analyses. 

9.5.1 Recommended Methods for Long-Term Trend Analysis 

After the first three sampling years of monitoring data are collected at each large river park 

(SACN and MISS) and periodically thereafter, more-intensive analyses of change will be 

performed. In addition to repeated-measures, time-series, regression, and non-parametric 

equivalents of various methods such as ANOVA and t-tests, monitoring data may also be 

evaluated through Monte Carlo simulation analyses, Bayesian analyses, and comparisons of 

period means. For the latter-most approach, one is often interested in comparing values before 

and after an important event (e.g., change in management policy, remarkable anthropogenic 

disturbance, natural catastrophe, drought). Years are then considered as replicates within each of 

the two periods. Trends in parameters will be analyzed with respect to biotic and abiotic 

covariates, although cause-effect relationships may be investigated more thoroughly by NPS 

partners and collaborators (e.g., USGS-WRD, university investigators). 

In addition to analyzing each variable separately, flow-adjusted water-quality variables that are 

not correlated and that naturally could be considered a homogeneous group of parameters could 

be analyzed collectively through multivariate ordinations (e.g., nonmetric multi-dimensional 

scaling, NMDS; McCune and Grace 2002) of resource conditions through time. This approach 

effectively integrates information across many indicators, and can suggest whether individual 

stations are all moving in the same direction in multidimensional ordination space. Furthermore, 

joint plots can be overlaid on the ordination, and can suggest which variables correlate most 

strongly to the direction of changes. Similarly, if specific comparisons were desired across a 

suite of uncorrelated variables, two or more pre-defined groups of samples could be compared 

using MANOVA or NPMANOVA, depending on whether parametric assumptions are met 

(Sokal and Rohlf 1995; Zar 2007). 

9.5.2 Approaches to Analyze Frequently-Collected Data 

In contrast to many other parameters that GLKN is monitoring, water-quality measurements 

from the three non-wadeable rivers are (and have been for many years) collected many times per 

year. Not only does the long-term nature of this dataset allow for robust retrospective analyses of 

trend, but the multiple sampling sessions within each year allow for various approaches to 

analyze long-term trends. For example, if the goal is to monitor trend in the average value of a 

particular water-quality parameter, then all measurements collected within the year at each 

sampling location would be considered temporal subsamples and would be averaged. Trend 

analysis (using repeated-measures, time-series, or other regression analyses) would thus be 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #9, page 4

performed simply on the annual means at each sampling location. This approach seems 

particularly viable for parameters that do not exhibit strong intra-annual variability (e.g., pH). In 

contrast, this approach may be vulnerable to imprecision or bias if a parameter exhibits 

significant, predictable variability in its value throughout the year and data are not collected at a 

high number of intended sampling occasions. 

Alternatively, if a particular parameter is known to exhibit significant intra-annual variability 

(e.g., phosphorus concentration), samples within the year can be partitioned into one of several 

periods (ideally, defined by relevant phenological or biological phenomena). Thus, for example, 

if interannual trends in nutrient concentrations during algal blooms are of interest, the temporal 

domain can be accordingly defined, and all samples within that window averaged within each 

year and the means analyzed for trend across years. Finally, if there is a strong desire to 

incorporate intra-annual variability into interannual trend analyses, data within each year can be 

analyzed through a smoothing algorithm, and interannual variability is thus analyzed on the 

smoothed data. It may be the case, however, that process variation is larger than the sampling 

variability (Burnham et al. 1987). 

9.5.3 Duplicate Sampling 

To ensure that understanding of water quality trends within lakes of the GLKN is not 

confounded by biased results, we will collect duplicate samples and field measurements at the 

rate of approximately once every 10 samples. We will assess the relative percent difference 

between duplicate samples or measurements and flag data that do not meet the QA/QC 

guidelines detailed in SOP #12. Those data that do not meet the QA/QC stipulations may or may 

not be used in analyses, on a case by case basis. For example, parameters measured at low 

concentrations (e.g., less than five times the method detection limit) may be accepted, and both 

duplicates used in analysis. If duplicate samples meet the QA/QC guidelines, we will use the 

mean value of the duplicate measurements in data analyses. Explanations of how duplicates are 

handled in data analyses will be included in reports. 

9.5.4 Other Analytical Considerations 

For trend analyses performed using regression, trend will be investigated using a linear 

relationship. If analyses suggest a non-linear temporal pattern, serial autocorrelation, or lagged 

response to stressors, appropriate analytical modifications will occur. Adopting the philosophies 

of the precautionary principle (United Nations 1992) and the safe minimum standard of 

conservation (Ciriacy-Wantrup 1952; Berrens et al. 1998), the GLKN monitoring program seeks 

to identify potential natural resource problems early, before deleterious or irreversible ecosystem 

changes occur. Consequently, for most analyses that use the null hypothesis of no change 

through time, we will adopt α = 0.10. Furthermore, for particularly variable parameters that are 

measured at relatively few stations, magnitudes of change that seem biologically meaningful 

(Johnson 1999) yet have 0.10 < α < 0.20 may nonetheless merit either increased attention (e.g., 

more extensive sampling) in future monitoring or experimental study. If water-quality 

monitoring tracks a relatively large suite of variables, Bonferroni or modified Bonferroni 

corrections (e.g., Hohm’s method) may be performed, to maintain the ‘familywise’ alpha at 0.10. 

This is because, if 20 ecological variables were monitored at an alpha of 0.10, two of them would 

be expected to apparently exhibit ‘significant’ trends, when none of them had any actual trend. 

Roback and Askins (2005) argue, however, that if the main goal is simply initial screening for 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #9, page 5

conservation problems or generation of hypotheses to be tested further (but not detection of real 

differences or trends), then alpha can be left at its standard comparisonwise significance level, to 

avoid Type II errors. 

Lotic systems are dynamic when compared to their more static lentic counterparts; water moves 

through the river network relatively quickly, with a finite residence time. Therefore, 

measurements taken during the year at a particular station would constitute temporal subsamples 

rather than replicates (unless the domain of interest is only within that particular year, in which 

case the measurements would be independent, repeated measures). Repeated samples at a 

particular location would be likely to exhibit less correlation with each other than to samples at 

other points in the domain sampled at the same time. There are, however, analytical frameworks 

(e.g., repeated measures) that can accommodate multiple samples taken from the same location. 

When the dataset contains non-detects, we will follow Helsel (2005) in conducting statistical 

analyses. Several methods exist for handling non-detects, each with advantages and drawbacks. 

Early in our program we will likely use a substitution method, where a value between zero and 

the detection limit will be substituted for the non-detect. The main drawback of this method is 

that estimates of the true variability are not possible. When the program is more mature and we 

have adequate data to determine the distribution of data, we will likely use maximum likelihood 

estimation, which works well for large sample sizes. Other methods, such as “regression on order 

statistics” and the non-parametric Kaplan-Meier method will be considered, and in consultation 

with a statistician, the most appropriate method for the data will be employed. 

9.6 Literature Cited 

Berrens, R. P., D. S. Brookshire, M. McKee, and C. Schmidt. 1998. Implementing the safe 

minimum standard approach. Land Economics 74:147-161. 

Burnham, K. P., D. R. Anderson, G. C. White, C. Brownie, and K. H. Pollock. 1987. Design and 

analysis of fish survival experiments based on release-recapture data. American Fisheries 

Society Monograph 5:1-437. American Fisheries Society, Bethesda, Maryland. 

Ciriacy-Wantrup, S. V. 1952. Resource conservation: economics and policies. University of 

California Press, Berkeley, California. 

Guthery, F. S., J. J. Lusk, and M. J. Peterson. 2001. The fall of the null hypothesis: liabilities and 

opportunities. Journal of Wildlife Management 65:379-384. 

Helsel D. R. 2005. Nondetects and data analysis: Statistics for censored environmental data. John 

Wiley & Sons, Inc., New York. 

Johnson, D. H. 1999. The insignificance of statistical significance testing. Journal of Wildlife 

Management 63:763-772. 

MacCluskie, M., K. Oakley, T. McDonald, and D. Wilder. 2004. Vital Signs Monitoring Plan 

Phase III Report. National Park Service, Central Alaska Network, Fairbanks, Alaska. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #9, page 6

Magdalene, S., D. R. Engstrom, and J. Elias. 2008. Large rivers water quality monitoring 

protocol. Version 1.0. National Park Service, Great Lakes Network, Ashland, Wisconsin. 

NPS/GLKN/NRR—2008/060. National Park Service, Fort Collins, Colorado.

McCune, B., and J. B. Grace. 2002. Analysis of ecological communities. MjM Software Design. 

Gleneden Beach, Oregon. 

Roback, P. L., and R. A. Askins. 2005. Judicious use of multiple hypothesis tests. Conservation 

Biology 19:261-267. 

Sokal, R. R., and F. J. Rohlf. 1995. Biometry: the principles and practice of statistics in 

biological research, 3rd ed. W.H. Freeman and Company, New York. 

United Nations. 1992. Agenda 21. Chapter 17 in Report of the United Nations conference on 

environment and development. United Nations, New York. 

Zar, J. H. 2007. Biostatistical analysis, 5th ed. Prentice-Hall, Inc., Upper Saddle River, New 

Jersey. 
Standard Operating Procedure #10: 

Reporting 

Version 1.0 

In Large Rivers Water Quality Monitoring Protocol 

Prepared by 

Suzanne Sanders and Joan Elias 

National Park Service 

Great Lakes Inventory and Monitoring Network 

2800 Lake Shore Drive East 

Ashland, Wisconsin 54806 

joan_elias@nps.gov 

August 2008 

Suggested citation: Sanders, S., and J. Elias. 2008. Standard operating procedure #10: 

Reporting. in Magdalene S., D.R. Engstrom, and J. Elias. 2008. Large rivers water quality 

monitoring protocol, Version 1.0. National Park Service, Great Lakes Network, Ashland, 

Wisconsin. NPS/GLKN/NRR—2008/060. National Park Service, Fort Collins, Colorado.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #10, page ii

Contents 

 Page

Revision History Log..................................................................................................................... iii 

10.0 Introduction..........................................................................................................................1 

10.1 Annual Summary Reports....................................................................................................1 

10.2 Analysis and Synthesis Reports...........................................................................................1

10.3 Scientific Journal Articles....................................................................................................2 

10.4 Other Communications ........................................................................................................2 

10.5 Literature Cited ....................................................................................................................3 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #10, page iii

Revision History Log 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project manager must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the header of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log: 

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 

.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #10, page 1

10.0 Introduction 

A primary goal of the NPS Servicewide I&M Program is to ensure that the results and 

knowledge gleaned from monitoring are shared with all appropriate parties, especially the parks 

and their natural resource managers. Because the Network’s main focus is to assist parks with 

monitoring needs, we will strive to provide park managers with clear, meaningful products to 

convey our findings. 

While the Network primarily addresses concerns of the parks, its monitoring program has the 

potential to serve a much broader community. For example, monitoring projects can provide a 

starting point for external scientific research (especially to establish cause-effect relationships), 

and can provide insights for adaptive management on other public lands. The Network is also 

accountable to multiple organizations within the federal government, including the NPS I&M 

Program and the U.S. Congress. To ensure accountability and to meet the requests of all parties, 

we will provide the types of reports and communications detailed below. 

10.1 Annual Summary Reports 

A summary report will be produced annually for the large rivers water quality Vital Signs 

monitored during the previous year. The primary audience for the annual summary reports will 

be parks. These summaries will be communications to document our efforts and convey the 

findings of the previous field season. At a minimum they will provide: 

• a brief introduction that describes why that Vital Sign is being monitored; 

• an outline of the sampling strategy, including the number of sites sampled, parameters 

measured, and analyses performed; 

• data summaries, including tables and figures to enhance visual presentation, as well as a 

text explanation of the findings; 

• any other relevant or significant findings; and 

• a limited discussion section in which important results are interpreted. 

The project manager will take the lead in writing the report and will coordinate an internal 

review. The reports will be provided to parks as soon as possible following the completion of 

each field season.

10.2 Analysis and Synthesis Reports 

Detailed reports in which data are analyzed and synthesized will be produced on a periodic basis, 

with the frequency depending on the given Vital Sign. The first analysis and synthesis reports 

will be written after at least three years of water quality data have been collected at a given park. 

The frequency of subsequent detailed reports will depend on the data and whether or not trends 

seem to be occurring. As the two large rivers parks are monitored repeatedly, in-depth analyses 

will be conducted for each park as well as both parks combined.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #10, page 2

The reports will be written in the format of a scientific journal article (abstract, introduction, 

methods, results, discussion, literature cited) and will contain in-depth analyses as outlined in the 

protocol (Magdalene et al. 2008) and SOP #9, Data Analysis. Further, these comprehensive 

reports will: 

• place the observed results in both a regional and historical context by relating them to 

other published literature, 

• discuss the significance of the results in terms of environmental change, and 

• provide management recommendations based on the findings. 

The project manager will take the lead in writing the analysis and synthesis reports, and will 

coordinate an internal review. The target audience of these reports will be the parks (primarily 

the natural resource managers), the Network, and both regional and Servicewide I&M programs. 

Outside of the park service, the target audience includes the Minnesota Pollution Control 

Agency, the Wisconsin Department of Natural Resources, the St. Croix River Interagency Basin 

Team, the Twin Cities Metropolitan Council, and the broader scientific community. 

Drafts of analysis and synthesis reports will be reviewed internally and possibly sent to outside 

sources for further review, depending on how analytically complicated the methods are and on 

the gravity of the implications and recommendations.. 

10.3 Scientific Journal Articles 

Because the monitoring protocol for large rivers has been designed with rigorous standards for 

sampling design and analysis, monitoring results are expected to be highly defensible and meet 

the standards of the peer-review process. The publication of monitoring results in scientific 

journals will allow the Network to reach the scientific community in a way that internal NPS 

reports cannot. Further, peer-reviewed publications can promote collaborative investigation by 

members of the scientific community, either independently or in cooperation with the Network. 

Ultimately, this process should foster a greater understanding of ecosystem components and 

processes. 

For these reasons, the Great Lakes I&M Network will strive to publish analysis and synthesis 

reports in peer-reviewed scientific journals. We will encourage the preparation of manuscripts by 

having reviewers of analysis and syntheses reports recommend whether publication is warranted 

and suggest appropriate journals. The Network’s aquatic ecologist and coordinator will track 

these recommendations and encourage and provide work time respectively.

10.4 Other Communications 

While reports are a definitive method of documenting the progress of each program, other means 

of communication can further disseminate information to a broader audience. To this end, we 

will provide the following additional types of communications: 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008

SOP #10, page 3

Briefings to Park Biologists 

The project manager will present the findings from the water quality monitoring program to the 

biologists from the parks in which monitoring was conducted the previous year. These 

presentations, which will likely occur at the annual technical committee meeting in March, will 

provide a concise synopsis of monitoring results as well as management considerations. 

Conference Presentations 

When possible, the project manager will present monitoring results at regional and national 

scientific conferences. Such presentations will allow the Network to reach the broader scientific 

community, as well as land managers and conservation practitioners. Potential conferences 

include those sponsored by the Ecological Society of America, Society for Conservation 

Biology, The Wildlife Society, the Natural Areas Association, the NPS Water Professionals 

Meeting, and the George Wright Society. At a more local scale, the Western Great Lakes 

Research Conference, which is sponsored in part by the Network, is a valuable venue for 

information exchange.

10.5 Literature Cited 

Magdalene, S., D. R. Engstrom, and J. Elias. 2008. Large rivers water quality monitoring 

protocol. Version 1.0. National Park Service, Great Lakes Network, Ashland, Wisconsin. 

NPS/GLKN/NRR—2008/060. National Park Service, Fort Collins, Colorado. 
Standard Operating Procedure #11: 

Post-Season Procedures 

Version 1.0 

In Large Rivers Water Quality Monitoring Protocol 

Prepared by 

Richard Axler and Elaine Ruzycki 

University of Minnesota-Duluth, Natural Resource Research Institute 

5013 Miller Trunk Highway 

Duluth, Minnesota 55811 

and 

Joan Elias (contact author) 

National Park Service 

Great Lakes Inventory and Monitoring Network 

2800 Lake Shore Drive East 

Ashland, Wisconsin 54806 

joan_elias@nps.gov 

August 2008 

Suggested citation: Axler R., Ruzycki E., and Elias J. 2008. Standard operating procedure #11: 

Post-season procedures. in Magdalene S., D.R. Engstrom, and J. Elias. 2008. Large rivers water 

quality monitoring protocol, Version 1.0. National Park Service, Great Lakes Network, Ashland, 

Wisconsin. NPS/GLKN/NRR—2008/060. National Park Service, Fort Collins, Colorado.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #11, page ii

Contents 

 Page

Revision History Log..................................................................................................................... iii 

11.0 Introduction..........................................................................................................................1 

11.1 End of Season Procedures....................................................................................................1 

 11.1.1 Field Instruments and Equipment .............................................................................1 

 11.1.2 Laboratory Equipment ..............................................................................................1 

11.2 Data Management ................................................................................................................2 

11.3 Quality Assurance Quality Control......................................................................................2 

11.4 Literature Cited ....................................................................................................................2 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #11, page iii

Revision History Log 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project manager must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the header of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log: 

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #11, page 1

11.0 Introduction 

The proper maintenance and storage of field and laboratory equipment will prolong the life of 

the gear as well as simplify start-up procedures for the next field sampling season. 

11.1 End of Season Procedures 

11.1.1 Field Instruments and Equipment 

When multiprobe sondes are to be stored for extended periods of time, make the following 

preparations: 

• Thoroughly clean the sensors. 

• Remove installed batteries. 

• Be sure sensors remain moist by adding tap water to the storage cap. Use the amount of 

water recommended by the manufacturer. If the sensors might be exposed to freezing 

temperatures, use a solution of one-half tap water and one-half methanol. 

• Store away from direct sunlight. Although the instrument should be able to be reliably 

reactivated for field use with a minimum of effort before field use, it should be tested 

well in advance of scheduled surveys to allow time for repair or replacement. 

Refer to equipment manuals for more detailed instructions regarding maintenance of multiprobe 

sondes. 

End-of-season care of other equipment includes the following: 

• Inspect and clean all equipment following the procedures detailed in SOP #5, 

Decontamination of Equipment to Remove Exotic Species. This effort minimizes the 

potential for transferring nuisance species from contaminated river sections to 

uncontaminated sections. 

• Lay out all ropes and sampling lines to dry completely, then coil or roll back into their 

holders. 

• Store field equipment in protective storage cases to avoid damage. 

• Clean all sample collection and storage containers in a 0.1N HCl acid bath followed by 

deionized water rinses as per SOPs #6 and #7. 

• Return all of the equipment and supplies to the proper storage area. Keep them organized 

so they can be inventoried using the equipment and supply checklists. 

• Store calibration standards and electrolyte solutions in a temperature-controlled 

environment. 

• Properly dispose of all chemical waste material. 

11.1.2 Laboratory Equipment 

• Clean all labware in a 0.1N HCl acid bath followed by deionized water rinses as per SOP 

#7. 

• Inventory all supplies and replace if necessary as soon as possible. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #11, page 2

11.2 Data Management 

There is no substitute for complete and accurate record keeping of field-derived data. Field 

technicians, crew leaders, and project leaders share responsibility for collecting, verifying, and 

documenting data according to the guidelines in this monitoring protocol and all applicable 

standard operating procedures. Refer to the GLKN Data and Information Management Plan 

(Hart and Gafvert 2005) for overall guidance and follow SOP #8, Data Entry and Management

and SOP #10, Reporting, for additional details. 

11.3 Quality Assurance/Quality Control 

Taking proper care of all field and lab instrumentation and sampling gear is a fundamental part 

of any QA/QC program. Sensors that are properly cared for will likely be less variable and 

equilibrate more quickly in the field. See SOP #12 for additional details on QA/QC procedures. 

11.4 Literature Cited

Hart, M., and U. Gafvert. 2005. Data management plan: Great Lakes Inventory & Monitoring 

Network (draft). National Park Service Great Lakes Inventory and Monitoring Network 

GLKN/2005/20. 

Standard Operating Procedure #12: 

Quality Assurance/Quality Control 

Version 1.0 

In Large Rivers Water Quality Monitoring Protocol 

Prepared by 

Tracy Ledder and Joan Elias (contact author) 

National Park Service 

Great Lakes Inventory and Monitoring Network 

2800 Lake Shore Drive East 

Ashland, Wisconsin 54806 

joan_elias@nps.gov 

August 2008 

Suggested citation: Ledder T., and J. Elias. 2008. Standard operating procedure #12: Quality 

assurance/quality control. in Magdalene S., D.R. Engstrom, and J. Elias. 2008. Large rivers water 

quality monitoring protocol, Version 1.0. National Park Service, Great Lakes Network, Ashland, 

Wisconsin. NPS/GLKN/NRR—2008/060. National Park Service, Fort Collins, Colorado.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page ii 

Contents 

 Page

Revision History Log..................................................................................................................... iv 

Acknowledgements..........................................................................................................................v 

12.0 Purpose.................................................................................................................................1 

12.1 Applicability ........................................................................................................................1 

12.2 Summary..............................................................................................................................1 

12.3 Definitions and Abbreviations .............................................................................................2 

12.4 Personnel Responsibilities ...................................................................................................3 

12.5 Sampling Process and Design..............................................................................................4

 12.5.1 Site Selection ............................................................................................................5 

 12.5.2 Field Collection Parameters......................................................................................5 

 12.5.3 Field Analysis ...........................................................................................................6 

 12.5.4 Laboratory Analysis..................................................................................................7

12.6 Sampling Methods ...............................................................................................................9 

 12.6.1 Site Locations............................................................................................................9 

 12.6.2 Field Water Measurements .......................................................................................9 

 12.6.3 Samples for Laboratory Analysis............................................................................11 

 12.6.4 Sampling Forms......................................................................................................13

12.7 Handling and Custody........................................................................................................13 

 12.7.1 Field Data................................................................................................................13 

 12.7.2 Site/Sample Identity Codes.....................................................................................14 

 12.7.3 Data Transfer ..........................................................................................................14 

 12.7.4 Sample Transfer......................................................................................................14 

12.8 Analytical Methods............................................................................................................16 

 12.8.1 Field Methods .........................................................................................................16 

 12.8.2 Field Equipment Performance Criteria ...................................................................18 

 12.8.3 Laboratory...............................................................................................................19 

 12.8.4 Laboratory Performance Criteria ............................................................................19 

 12.8.5 Changing Methods and Documenting Cumulative Bias.........................................22 

12.9 Instrument Calibration Frequency, Inspection, and Maintenance .....................................23 

 12.9.1 Field Instruments ....................................................................................................23 

 12.9.2 Laboratory Instruments...........................................................................................23 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page iii 

Contents (continued) 

 Page 

12.10 Inspection and Acceptance of Supplies and Consumables................................................24 

12.11 Records Management.........................................................................................................24 

12.12 Assessment and Oversight .................................................................................................25 

 12.12.1 Corrective Responsive Actions.............................................................................25 

12.13 Reports to Management .....................................................................................................26 

12.14 Data Validation and Usability............................................................................................26 

12.15 Reconciliation with Data Quality Objectives ....................................................................27 

12.16 Literature Cited ..................................................................................................................27 

Attachment A. Checklists for field and laboratory method selection 

Attachment B. Checklists for data validation 

Tables 

 Page 

Table 1. Number of randomly and non-randomly selected monitoring stations .............................5 

Table 2. Panel array of sampling frequency and return period........................................................6 

Table 3. Field variables and required in situ measurement methods...............................................6 

Table 4. Typical sensor performance specifications for multiprobes..............................................7 

Table 5. Analytical detection levels required for GLKN water quality monitoring........................8 

Table 6. Recommended instrument stabilization criteria for recording field measurements ........10 

Table 7. Example range of analytical methods, MDLs, containers, and holding times ................12 

Table 8. STORET-supported laboratory remark codes .................................................................15 

Table 9. STORET detection descriptors ........................................................................................15

Table 10. Field instrument ideal calibration frequencies and acceptance criteria .........................17 

Table 11. Frequency, acceptable range, and corrective actions for QC samples...........................21 

Table 12. Checklists of equipment and supplies............................................................................24 

Table 13. Summary of QA/QC procedures pertaining to data management .................................25 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page iv 

Revision History Log 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project leader and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log: 

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page v 

Acknowledgements 

This document was prepared largely through the use of available National Park Service guidance 

and documents prepared for the Great Lakes Network Inventory and Monitoring program. The 

authors wish to acknowledge these sources and thank them for the valuable contribution that they 

have made to this document. Some verbiage contained within this standard operating procedure 

(SOP) was first written in the protocol narrative and other SOPs, and we wish to thank the 

authors of those sections. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 1 

12.0 Purpose 

This standard operating procedure (SOP) defines procedures for quality assurance and quality 

control to be used with the Great Lakes Network protocol for monitoring water quality in large 

rivers. Quality assurance is the planned and systematic pattern of all actions necessary to provide 

adequate confidence, or assurance, that a project outcome optimally fulfills expectations. Quality 

control is the systematic evaluation of the various aspects of a project to ensure, or control, that 

the standards of quality are being met. Quality control involves specific tasks undertaken to 

determine the reliability of field and laboratory data. Together, quality assurance/quality control 

(QA/QC) is a substantial part of any monitoring program. The objective of QA/QC is to ensure 

that the data generated by a project are meaningful, representative, complete, precise, 

comparable, scientifically defensible, and reasonably free from bias (Irwin 2006). 

12.1 Applicability 

Procedures in this SOP will be implemented during all work pertaining to monitoring water 

quality in inland lakes as described in the protocol narrative. This SOP is designed to assure that 

all data obtained will contribute quality information to an understanding of the ecological 

integrity of park units of the Great Lakes Network. 

The rationale for dividing a sampling protocol into a protocol narrative with supporting SOPs is 

based on the following: 

• The protocol narrative is a general overview of the protocol that gives the history and 

justification for doing the work and an overview of the sampling methods, but does not 

provide all methodological details. The protocol narrative will only be revised if major 

changes are made to the protocol. 

• The SOPs are specific step-by-step instructions for performing a given task. They are 

expected to be revised more frequently than the protocol narrative. 

• Usually, when a SOP is revised, it is not necessary to revise the protocol narrative to 

reflect the specific changes made to the SOP. All versions of the protocol narrative and 

SOPs will be archived. 

The steps for changing the protocol (either the protocol narrative or the SOPs) are outlined in 

Procedures for Revising the Protocol (SOP #13). 

12.2 Summary 

The monitoring protocol is intended to document river water quality status and trends for 

individual stations, on a longitudinal (downstream) basis, and a park-wide basis. The protocol 

includes historical analysis, sample design, field and laboratory methods, data analysis and 

reporting, and training and operational requirements. The protocol objectives and specific 

monitoring questions are outlined below. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 2 

Objectives 

1) Gather flow data for the St. Croix, Namekagon, and Mississippi Rivers to determine 

changes in mean monthly and mean annual flows. 

2) Monitor mean annual concentrations of core and advanced suite parameters in MISS and 

SACN and from the mouths of selected tributaries, accounting for seasonality in water 

quality conditions. 

3) Relate current water quality conditions to known historical conditions. 

4) Analyze water quality parameters for trends, and correlate any observed trends with 

potential causes (such as weather, climate, land use, point sources, exotic species, and 

atmospheric deposition). 

Monitoring Questions

1) What are the current status and long-term trends in systematic flow regime? 

2) What are the current status and long-term spatial and temporal trends in select water 

quality variables, including temperature, pH, specific conductance, dissolved oxygen, 

water clarity, sediment, alkalinity, major ions, and nutrients? 

3) Are changes in water quality parameters correlated with tributary influences or changes 

in other aspects of the ecosystem, such as measures of biotic communities, exotic species, 

land use or land cover, weather and climate, or atmospheric deposition? 

12.3 Definitions and Abbreviations 

Blanks ....................................analytical quality control samples analyzed in the same manner as 

site samples 

Equipment or field blank .......sample of distilled, deionized water taken to the field opened and 

used as sample water would be (i.e., poured through equipment 

used to handle samples) 

Trip blank...............................used to indicate potential contamination due to migration of 

volatile organic chemicals (VOCs) from the air on the site or 

shipment into the sample vial. Consists of laboratory distilled, 

deionized water in a 40-mL glass vial sealed with a Teflon septum 

and is unopened in the field. 

Laboratory calibration blank...distilled, deionized water injected directly into an instrument, 

indicates contamination in instrument or source of water 

Laboratory reagent blank .......or method blank, distilled, deionized water manipulated as if it 

were a sample (digestions, extractions, etc.) 

cfs...........................................cubic feet per second 

CCV .......................................Continuing Calibration Verification 

EPA........................................Environmental Protection Agency 

EMAP ....................................Environmental Monitoring and Assessment Program 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 3 

GLKN ....................................Great Lakes Inventory and Monitoring Network 

m ............................................meter 

MDL.......................................Method Detection Limit 

mg/L.......................................milligrams per liter 

MISS ......................................Mississippi National River and Recreation Area 

ML..........................................Method Limit of quantitation 

MSDS.....................................Material Safety Data Sheet 

NAWQA ................................National Water Quality Assessment Program 

NPS ........................................National Park Service 

NPSTORET ...........................National Park Service Storage and Retrieval Database 

QA/QC ...................................Quality Assurance/Quality Control 

QAPP .....................................Quality Assurance Project Plan 

Reference standard.................independently created solution of known concentration 

SACN.....................................St. Croix National Scenic Riverway 

SOP ........................................Standard Operating Procedure 

STORET ................................Storage and Retrieval Database 

USGS .....................................United States Geological Survey 

μg/L........................................micrograms per liter 

12.4 Personnel Responsibilities 

Personnel will study this SOP prior to beginning work on the project and follow its procedures in 

order to conduct the project according to outlined QA/QC procedures. This will ensure 

consistency and comparability when changes in personnel occur. 

Field personnel should be adequately experienced and/or trained in using field and water quality 

sampling equipment. This experience is best obtained through a combination of classroom and 

hands-on training, including pilot-testing equipment at a nearby waterbody. Personnel should be 

familiar with the instruction manuals for all equipment, particularly with regard to calibration 

and maintenance procedures. See SOP #2, Training and Safety, for more details on training. 

The role of the project manager is to serve as a liaison among other related water quality 

monitoring projects conducted by partners (e.g., state monitoring programs), park staff, other 

Network staff (field personnel, data manager), a contracted analytical laboratory, and other 

GLKN monitoring project managers. The individual will coordinate with resource management 

staff at the parks to ensure parks are informed of monitoring activities. Specific responsibilities 

of the project manager include the following: 

• Coordinate field schedules and availability of supplies with field personnel 

• Develop a training program for field personnel 

• Develop, document, and oversee the implementation of standard procedures for field data 

collection and data handling 

• Coordinate logistics with park staff 

• Develop quality assurance and quality control measures for the project, supervise staff 

training and conduct quality assurance checks of field sampling techniques at least once, 

mid-season, with each field crew 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 4 

• Contract with an analytical laboratory for analysis of water samples, ensure lab results 

meet program needs (e.g., QA/QC procedures, meaningful minimum detection limits for 

low level strength waters, adequate reproducibility of replicate samples) 

• Supervise or perform data entry, verification, and validation 

• Summarize and analyze data, prepare reports 

• Serve as the main point of contact concerning data content 

The project manager will also work closely with the data manager in the following capacities: 

• Complete project documentation in NPSTORET (describing who, what, where, when, 

why and how of a project) 

• Develop data verification and validation measures for quality assurance 

• Ensure staff are trained in the use of database software and quality assurance procedures 

• Coordinate changes to the field data forms and the user interface for the project database 

• Identify sensitive information that requires special consideration prior to distribution 

• Manage the archival process to ensure regular archival of project documentation, original 

field data, databases, reports and summaries, and other products from the project 

• Define how project data will be transformed from raw data into meaningful information 

and create data summary procedures to automate and standardize this process 

• Establish meaningful liaisons with state counterparts to promote sharing of data on a 

timely basis 

The assistant project manager will be responsible for preparing supplies and equipment for the 

field season; ordering needed supplies; making travel arrangements; maintaining sampling 

equipment; maintaining field vehicles; ensuring field personnel follow sampling protocols; 

preparing field data forms, chain of custody forms, and analytical service request forms for each 

site; notifying contract laboratory of planned sample shipment date; and providing project 

manager with field trip and check-in schedule. 

Field personnel will be responsible for following protocols and standard operating procedures 

during field activities and the handling of samples. 

Roles of staff are explained in more depth in section five of the large rivers protocol narrative, 

along with training and requirements. 

12.5 Sampling Process and Design 

Two major ecological monitoring programs (the USGS National Water-Quality Assessment 

(NAWQA) program and the EPA Environmental Monitoring and Assessment Program-Aquatic 

Resource Monitoring (EMAP-ARM)) use different site-selection methods. The GLKN goal is to 

combine the strengths of both programs for monitoring water quality of lotic systems in the NPS 

Great Lakes Network. For further information see the large rivers protocol narrative. 

The information goals and statistical requirements determine the sampling frequency. To identify 

the long-term trends in a stream or river, the sampling frequency should be sufficient to identify 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 5 

a statistical trend beyond the background variability of a dynamic flow system. Therefore, it is 

essential to evaluate existing data prior to establishing 1) the number of sites and 2) the 

frequency of sampling. Statistical power analysis based on the power to detect change guides the 

selection of these two parameters, using calculations of statistical sample size and analysis of 

sensitivity to sampling frequency, respectively. The goal is to be able to detect 20% change at 

80% power and 5% significance. Due to natural variability of the different parameters, the 

number of sampling sites and sampling duration time required to detect this level of change for 

all parameters of interest may not be possible within budget constraints. 

12.5.1 Site Selection 

This program includes both randomly-selected and nonrandomly-selected sites. All sites will be 

analyzed on an individual basis, to determine water quality trends at each location. Only the 

randomly-selected sites will be grouped for analysis of population statistics and trends. (See the 

large rivers protocol narrative, section two, for details.) 

The GLKN monitoring sites for MISS and SACN are mapped in the protocol narrative. Six 

randomly-selected sites and five to seven nonrandom sites comprise the SACN sampling design. 

Adding five nonrandom monitoring stations to on-going efforts in MISS will substantially close 

gaps in the existing monitoring programs; GLKN budget constraints make random sampling 

unfeasible at this park. In summary, Table 1 lists the number of each station type (random or 

nonrandom) and the total number of monitoring stations for each park unit. All site locations 

described in the protocol narrative were field-verified for representativeness and accessibility 

before being finalized and accepted as a new monitoring station. 

Table 1. Number of randomly-selected and nonrandomly-selected monitoring stations for the 

Upper SACN, Lower SACN, and MISS park units. 

Station Type 

Upper 

SACN 

Lower 

SACN MISS 

Random 3 3 0 

Nonrandom 5 (7) 5 

TOTAL 11 (13) 5 

12.5.2 Field Collection Parameters 

Samples will be collected monthly for nutrients, chlorophyll-a, and total suspended solids during 

the open water season, which is usually March through November, monitoring spring, summer, 

and autumn flows. The core water quality suite (dissolved oxygen, temperature, specific 

conductance, pH, flow, and clarity) will also be monitored monthly. Water samples for 

laboratory analysis of major cations and anions, alkalinity, dissolved silica, and dissolved 

organic carbon will be collected quarterly, or three times during the open water season. 

Randomly-selected and nonrandomly-selected stations in each park unit will be sampled on the 

same frequency and at the same time each sampling period. The current large river monitoring 

plan is to sample from one park unit each year, alternating between SACN and MISS. Table 2 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 6 

summarizes the large rivers sampling frequency and sampling return period in a panel array. 

Eventually, the Network will coordinate large river sampling events with other vital signs 

monitoring projects, such as aquatic biota. 

Table 2. Panel array of sampling frequency and return period for the large river parks, SACN and 

MISS. M = monthly sampling for nine months, March through November, Q = quarterly 

sampling March, June, and September. 

Monitoring Year 

Park Unit WQ Variables 1 2 3 4 

MISS Core suite M M 

 Nutrients M M 

 Total chlorophyll-a M M 

 Total suspended solids M M 

 Major ions Q Q 

 Alkalinity Q Q 

 Dissolved organic carbon Q Q 

 Dissolved silica Q Q 

SACN Core suite M M 

 Nutrients M M 

 Total chlorophyll-a M M 

 Total suspended solids M M 

 Major ions Q Q 

 Alkalinity Q Q 

 Dissolved organic carbon Q Q 

 Dissolved silica Q Q 

12.5.3 Field Analysis 

Dissolved oxygen, temperature, specific conductance, turbidity, and pH will be measured in the 

field using a multiprobe and following the methods listed in Table 3. Multiprobes typically 

perform within the specifications detailed in Table 4. Other parameters may be analyzed at the 

field station by field personnel in the future. 

Table 3. Field variables and required in situ measurement method. 

Field Variable Method 

Temperature (°C) EPA 170.1 

pH (standard units) EPA 150.1 

Specific conductivity (μS/cm) EPA 120.1 

Dissolved oxygen (mg/L) EPA 360.1 

Clarity (cm) Transparency tube 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 7 

Table 4. Typical sensor performance specifications for multiprobe field instruments. 

Sensor 

Expected 

Range 

Reporting 

Resolution* Estimated Bias Stabilization Criteria 

Temperature -5 to 45 °C 0.01 °C ±0.15 °C Thermistor: ± 0.2 °C 

Glass: ± 0.5 °C 

Specific 

Conductivity 

(SC25) 

0 to 2000 

μS/cm 

μS/cm 

(range 

dependent) 

±0.5% of reading 

+ 1 μS/cm 

≤100 μS/cm: ± 5% 

>100 μS/cm: ± 3% 

pH 1 to 14 units 0.01 unit ±0.2 units ± 0.1 standard unit 

Dissolved 

Oxygen (Conc.) 0 to 50 mg/L 0.01 mg/L 

0 to 20 mg/L: 

±0.2 mg/L 

20 to 50 mg/L: 

±0.6 mg/L 

± 0.3 mg/L 

Dissolved 

Oxygen (% sat.) 0-200% 0.1% ~ ±2 % ± 2 % 

Depth – Z 

(pressure 

sensor) 

0 - > 100 m 0.1 m ~ 0.1 m 0.1 m 

* Resolution specifications are supplied by the manufacturers of the measuring meters. They are not necessarily closely related to 

real-world (outdoor) precision or bias, and are sometimes more related to the number of significant figures reported rather than 

how accurate the extra significant figures are. This is why we will control measurement sensitivity in the actual outdoor 

measuring environment at least once a year by calculating alternative measurement sensitivity (AMS; see Irwin 2006 for more 

details on AMS). 

Specification of quantification ability for field multiprobes is not a straightforward data quality 

objective exercise. Most field parameters tend to be those that characterize the waterbody and are 

not usually based on a criterion limit as would be used for a toxic pollutant. Therefore, 

instrument selection should be based on the parameters and ranges they can measure, but 

instrument-specific estimations of the range of uncertainty for each parameter will have to be 

made when interpreting data. Details on estimating instrument sensitivity are included below in 

section 12.8.2. 

12.5.4 Laboratory Analysis 

Samples will be collected in the field according to SOP #6 for shipment to a contract laboratory 

that meets QA/QC requirements outlined in Section 12.8.4 of this SOP. Samples will be 

analyzed for nutrients (TP, TN, NO3+NO2-N, NH4-N), total chlorophyll-a, and total suspended 

solids monthly, while alkalinity, major ions (Cl-

, SO4

2-, Ca2+, Na+

, K+, and Mg2+), DOC, and 

SiO2, which tend to be less variable, will be monitored quarterly. 

Methods chosen will meet quantification limits according to the criteria tabulated below (Table 

5). The method limit of quantitation (ML) of the chosen method should be two to ten times lower 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 8 

than the typical expected low value. The ML is the lowest value that can be quantified with 

certainty. The value in the “ML needed” column of Table 5 is two to ten times lower than the 

lowest value found in the pilot year of sampling water quality for each analyte. This estimation is 

used as guide to the selection of the method that will be needed for this project. 

Table 5. Analytical detection levels required for GLKN water quality monitoring. 

Analyte Typical Low 

Value Found Criteria Sourcea, b Comment 

ML 

Needed 

Alkalinity 

(mg/L)c ND (<1) Lowest value 

pilot year MDL unknown 

DOC (mg/L) c 3 Lowest value 

pilot year Lab MDL 0.1 0.3 mg/L 

Ca2+ (mg/L) c 2.4 Horizon report MDL unknown 0.24 mg/L 

Cl-

 (mg/L) c 0.273 Lowest value 

pilot year Lab MDL 0.025 0.02 mg/L 

Chl-a (μg/L) 0.63 EPA Lower of VII and 

VIII 0.06 mg/L 

Cl-

 & SO4

2- 230 MN WQS Lowest of states 1.0 mg/L 

Mg2+ (mg/L) c 0.47 Horizon report MDL unknown 0.04 mg/L 

K+

 (mg/L) c 0.24 Lowest value 

pilot year Lab MDL 0.06 0.02 mg/L 

Na+

 (mg/L) c 0.5 Horizon report MDL unknown 0.05 mg/L 

SO4

2- (mg/L) c 0.625 Lowest value 

pilot year Lab MDL 0.025 0.06 mg/L 

TP (μg/L) 10 EPA Lower of VII and 

VIII 1.0 μg/L 

TN (mg/L) 0.38 EPA Lower of VII and 

VIII 0.03 mg/L 

NH4-N (ppb) c 0.005 Horizon report MDL unknown 0.001 μ g/L 

NO3+NO2-N 

(ppb) c .0002 Horizon report MDL unknown 0.0001 μ g/L 

Si02 (mg/L) ND (<0.1) Lowest value 

pilot year Lab MDL 0.2 0.1 mg/L 

NOTES: 

a: EPA = EPA Ecoregional nutrient criteria recommendations, lower value recommended for aggregate ecoregions VII and VIII 

(USEPA 2000). 

b: WQS = criteria value listed in Ledder (2003) state water quality standards 

c: parameter has no official criterion for any of the states, the value reported in the analytical requirement column is the lowest 

value determined in the pilot year for rivers or lakes or the lowest value found in a spot check of Horizon reports for each park. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 9 

The majority of the parameters listed in Table 5 are used in waterbody characterization and do 

not have criterion lower limits as would a toxic pollutant. Some of the criteria available are listed 

as maxima not to be exceeded and, as such, do not guide the selection of a method by ML. 

Guidelines to be used, therefore, include relevant state water quality standards, EPA eco-regional 

nutrient recommendations (USEPA 2000), state nutrient criteria as they are developed, data 

results for these parameters from the pilot studies carried out by GLKN, and/or lowest values for 

the parameter found in relevant Horizon reports (NPS 1995a, 1995b, 1995c, and 1999). 

12.6 Sampling Methods 

Consistent methods are important to long-term quality data. In actuality, the ideal conditions are 

not always met in the field or in the lab and changes in staff do occur. Therefore, documentation 

of procedures, site conditions, laboratory analysis, and reasons for deviations of any kind is 

important in and of itself for long-term projects. Personnel will be encouraged to write down 

more than they feel may be necessary in the moment as the future interpretation of their data will 

depend on the written record and not the memory of an individual. 

12.6.1 Site Locations 

Refer to description of monitoring station location, directions, and photos to verify correct 

location. Verify coordinates with a GPS unit. Document this verification. This information will 

be contained in a field binder along with a table of previous field measurements to compare with 

new measurements, and a discharge rating curve to verify new stage readings. 

Whenever possible, collect water samples from the centroid of flow, in a vertical profile of the 

water column. The centroid of flow is the midpoint of streamflow, or the point on the river’s 

cross-section perpendicular to flow that has equal volumes of flow to the right and to the left 

sides. Sampling from the centroid of flow assures that average water quality conditions are being 

sampled, and that water quality results are reasonably representative of average flow conditions 

at the particular site being sampled. 

Collect samples on the upstream side of the boat or bridge, to minimize contamination and 

disturbance. Avoid surfactants, floating debris, and turbid aeration when collecting samples. 

Rinse the integrating sampler and compositing jug three times with surface water before taking 

samples. Discard rinse water or excess sampling water on the downstream side of the boat. 

Allow any disturbed sediments to clear before taking the actual sample. Always follow 

procedures for minimizing contamination during the sampling process (See SOPs #5 and 6 for 

more details). 

12.6.2 Field Water Measurements 

Before making field measurements, properly-calibrated sensors (see SOP #6) must be allowed to 

equilibrate to the condition of the water being monitored. Sensors have equilibrated adequately 

when instrument readings have stabilized, that is, when the variability among measurements does 

not exceed an established criterion. The criteria for stabilized field readings were defined 

operationally by O’Ney (2005) for a set of three or more sequential measurements. The natural 

variability inherent in surface water or ground water at the time of sampling generally can be 

compared with these stability criteria and indirectly relates to the short term bias or the long term 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 10 

accuracy that should be attainable with a calibrated instrument. Dissolved oxygen typically 

requires a greater amount of time to stabilize than other parameters. In addition, differences in 

polarigraphic sensor membrane thicknesses, age, and rates of oxygen consumption increase the 

variability of the equilibration time. Depending on the site characteristics and the specific oxygen 

sensor, 3 to 5 minutes may be required for complete equilibration. This time far exceeds what is 

needed for the other parameters, which typically stabilize in less than 60 seconds. Observers 

should only note instrument dissolved oxygen readings after the stabilization criteria in Table 6 

are met, and then record readings for all parameters at once. 

Table 6. Recommended instrument stabilization criteria for recording field measurementsa,b. 

Standard Direct 

Field Measurement 

Stabilization Criteria 

(O’Ney 2005) 

Stabilization Criteria 

In situ Multisensors 

(WOW 2005) 

Temperaturec: 

Thermistor Thermometer 

Liquid-in-glass Thermometer 

± 0.2 °C 

± 0.5 °C 

± 0.2 °C 

(5%) 

Specific Conductivity (SC25)d

When ≤ 100 μS/cm 

When > 100 μS/cm 

± 5 % 

± 3 % 

< 5 uS/cm 

(10%) 

pHe

: Meter displays to 0.01 ± 0.1 unit ± 0.2 unit 

(10%) 

Dissolved oxygene

: 

Amperometric (same as 

polarigraphic) method ± 0.3 mg/L 

± 0.5 mg/L 

(10%) 

Notes: 

a: Resolution/sensitivity is a data quality indicator related to detection limits but typically handled differently for field probes 

than for laboratory parameters. For more information, see Irwin (2004). 

b: In the case of field probes, bias is typically a best case maximum deviation from known correct values (typically based on 

comparisons with known NIST certified reference materials or standards). True accuracy is a combination of high precision and 

low bias, and is hard to quantify with the small sample sizes used to control bias and precision in typical field measurements (see 

Irwin 2004 for more details). 

c: Recommended sensor calibration is quarterly. 

d: Recommended sensor calibration is daily. 

e: Recommended sensor calibration is at beginning of sampling day with a calibration check at the end of the day. 

Measure field water quality variables and conduct sampling according to SOP #6. Acquiring 

results of high quality requires consistent measurement methods and detection limits. 

Measurements should be made in the center of channelized flow, in a vertical profile of the water 

column. Begin just below the water’s surface (~ 0.3 m depth) and take readings after 

stabilization of the multiprobe. Lower the sensors to collect a vertical profile of field parameters 

at 1m intervals until 20m depth, and then every 2-5m depending on overall depth and gradients. 

Replicate 10% of the readings (e.g., at 1m, 10 m, etc.); take the replicate readings immediately 

following the original readings. Values should agree within 10% or the stabilization criteria in 

Table 6, whichever is larger. Use the transparency tube to measure the clarity of a sample 

collected with the integrating tube. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 11 

At all sites, record visual observation information required on the data sheet. Such observational 

data can provide important information to the interpretation of field measurements. 

At selected stations, record staff gage reading and/or take discharge measurements using a 

current flow meter. Select the appropriate piece of equipment and measurement intervals 

according to guidelines in SOP #6. Record information on a separate field form (Field Discharge 

Measurements). 

If any analyses are to be done in-house, conduct these analyses as soon as possible upon return 

from the field. A clean analytical station should be prepared in which to work, free of food items, 

mud, lubricants, or lab chemicals. Hands should be thoroughly washed. 

12.6.3 Samples for Laboratory Analysis 

Prepare bottles and labels prior to field sampling as per SOP #6. Collect samples on the upstream 

side of a bridge or boat from the center of channelized flow as per SOP #6. Prior to filling 

sample bottles sent by the laboratory, rinse the bottle once with sample water, if the bottle is not 

pre-preserved. Some analyses require preservation of the sample with acid, which may be added 

to the bottle by the contract laboratory; in these cases do not rinse the bottle first. Take care not 

to overfill the bottle if the bottle is pre-acidified, as overfilling will flood the acid out of the 

bottle. If the samples requiring acid preservation are not pre-preserved, use caution to add the 

ampule of preservative supplied by the lab and immediately rinse hands in water if acid is 

spilled. Protective gloves are recommended. 

Table 7 summarizes the variety of methods, detection limits, preservation techniques, and 

holding times for water samples addressed by this protocol. These methods conform to those 

used by Minnesota, Wisconsin, and Michigan for state certification of environmental laboratories 

involved in Clean Water Act or drinking water sample analysis (MDH 2005; WSLH 2003; 

MDEQ 2005). They are also used by EPA-funded research projects of natural waters in the upper 

midwestern U.S. Holding times shall in no case be less stringent than those recommended by 

EPA in 40 CFR Part 136 to 136.3 and appendices. Refer to SOP #6 for additional details 

regarding sample collection and preservation. 

Samples are stored in a cooler with ice packs during field sampling. Prepare samples for 

shipment according to the contract laboratory’s protocols. These protocols will be provided to 

the field sampling personnel for each sampling round so that the proper procedures are accessible 

in the event of contract laboratory changes. In general, samples are shipped on ice to maintain a 

temperature of approximately 4 °

C. A plastic bag is placed in the cooler first. Sample bottles are 

packed among sealable bags of ice and/or ice packs to prevent water leakage into sample bottle 

during shipment. Prepare a temperature check bottle for each anticipated cooler, if recommended 

by the contract analytical laboratory. Use tap water to fill an extra bottle of the same size used 

for one of the analytes and label as “Temperature Check”. Store this check bottle in the 

refrigerator with other samples; package and send to the analytical laboratory with the other 

samples. Some analyses require the sample to be frozen for shipment; such frozen samples are 

likewise packed among bags of ice and ice packs for shipment to the contract laboratory. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 12 

Table 7. Example range of analytical methods, method detection limits (MDLs), containers, and 

holding times. 

Analyte Analytical 

Note 1 Method # Det. Limit Vol. (ml) Filter Preservation 

Sample 

Bottle 

Note 2 

Hold 

Time 

Titrimetry 310.1 EPA-NERL 10 mg/L 4oC 14 days Alkalinity Spec. auto. 310.2 EPA-NERL 10 mg/L 4o

C 14 days 

 Titrimetry NFM USGS-OWQ 0.01 meg/L Note 4 None none 

ICP 3120B APHA 10 ug/L Note 3 pH<2 HNO3 P or G 6 mos 

Titrimetry 215.2 EPA-NERL 0.5 mg/L Note 3 4o Calcium C 6 mos 

FAA I-3152 USGS-NWQL 0.1 mg/L 250 Note 3 pH<2 HNO3 P 180 day 

IC 300.0 EPA-NERL 0.02 mg/L 4oC P or G 28 day 

Colorimetry 325.2 EPA-NERL 1 mg/L 4o Chloride C 28 day 

Titrimetry 4500-Cl APHA 0.15 mg/L 100 4oC P or G 28 day 

Chlorophyll-a Spect. 10200 APHA 2 ug/L < 1 L Note 4 Freeze filter P 30day 

Spect. 110.2 EPA-NERL 5 Pt units Note 5 4oC G 48 hours Color Vis. Comp. I-1250 USGS-NWQL 1 Pt-co 250 Note 5 4o

C P 30 days 

Spect. 415.3 EPA 0.018 mg/L 125 Note 3 pH<4 H2SO4 G 28 days DOC Spect. 0-1122-92 USGS 0.1 mg/L 4o

C AG 

ICP 3120B APHA 0.3 mg/L Note 3 pH<2 HNO3 P or G 6 mos K FAA 3111B APHA 5 ug/L Note 3 pH<2 HNO3 P or G 6 mos 

ICP 3120B APHA 20 ug/L Note 3 pH<2 HNO3 P or G 6 mos Mg FAA 3111B APHA 0.5 ug/L Note 3 pH<2 HNO3 P or G 6 mos 

ICP 3120B APHA 30 ug/L Note 3 pH<2 HNO3 P or G 6 mos Na FAA 3111B APHA 2 ug/L Note 3 pH<2 HNO3 P or G 6 mos 

Selective elec. 4500-NH3E 0.08 mg/L 4oC/pH2,0oC 24h/28d 

NH4-N Colorimetry 350.2 EPA-NERL 0.08 mg/L pH<4 H2SO4 28 day 

Titrimetry 4500-NH3 APHA 5 mg/L 4oC/pH2,0oC 24h/28d 

ICP 3120B APHA 20 ug/L Note 3 pH<2 HNO3 P or G 6 mos 

Spect. 4500- SiO2 D APHA 0.04 mg/L Note 3 No, 4o SiO2 C P 28 days 

FIA-Spect. 4500- SiO2 F APHA 0.78 ug/L Note 3 No, 4oC P 28 days 

TSS Gravimetric I-3765 USGS-NWQL 1 mg/L 250-

500 Note 4 4o

C filter P NA 

IC 4110C APHA 75 ug/L Note 3 pH<4 H2SO4 P or G 

SO4 CIE-UV D6508 ASTM 0.1 mg/L Note 3 pH<4 H2SO4 ASAP 

Spect. 37512 EPA-NERL 0.5 mg/L Note 3 pH<4 H2SO4 P or G 28 days 

Spect. I-2606 USGS-NWQL 0.001 mg/L 125 MgCl 4oC BrownP 30 days 

Alkaline P USGS 2003 0.01 mg/L 120 Note 6 4oC /H2SO4 TP 48 h/30d 

ICP 200.7 EPA-NERL 60 ug/L pH<2 HNO3 P 6 mos 

Alkaline P USGS 2003 0.03 mg/L 120 Note 6 4oC /H2SO4 48 h/30d 

Titrimetry 4500-N 0-100 mg/L 4o TN C AG 7 days 

Combustion 440.0 EPA-NERL 0.1 mg/L Filter 100 day 

Source: National Environmental Methods Inventory website (NEMI 2006) 

This list is not an endorsement of any particular method or laboratory for any particular analyte. Rather it is to be used as a

reference for the range of analytical methods available for each analyte. There are surface water conditions (pH, turbidity, other 

elements) that make a particular method unsuitable for a particular situation. As GLKN is monitoring surface water, the methods

listed were chosen as representative of the lower range of detection limits. 

Note 1. CIE-UV= capillary ion electrophoresis with UV detection, FAA = flame atomic absorption, FIA = flow injection 

analysis, IC= ion chromatography, ICP = inductively coupled plasma, Spec. auto = spectroscopy with autoanalyzer 

Note 2. P = plastic (polypropylene), G=glass, AG=amber glass 

Note 3. 0.45μm membrane filter. Pre-filter for dissolved portion analysis. 

Note 4. 0.45μm glass fiber filter. 

Note 5. 0.45μm membrane filter or centrifuge is recommended to remove suspended solids that affect color, however some color 

will also be removed. 

Note 6. USGS 2003. Evaluation of Alkaline Persulfate Digestion as an Alternative to Kjeldahl Digestion for Determination of 

Total and Dissolved Nitrogen and Phosphorus in Water By Charles J. Patton and Jennifer R. Kryskalla. U.S. Geological Survey 

Water-Resources Investigations Report 03-4174 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 13 

Follow the shipping company’s requirements in preparation of the cooler of samples for 

shipment. Packaging problems may cause delays in shipment, which can mean that samples do 

not arrive at the laboratory at the proper temperature or past holding time, compromising data 

quality. In general, the ice and samples should be contained within a sealed plastic bag within the 

cooler so that the cooler does not leak. Packing tape should be wrapped around the cooler 

vertically and around the lid seam horizontally to ensure it remains closed. A note on the cooler 

that it contains water samples is helpful as well so that if leakage occurs, carriers will know the 

contents are not hazardous. 

12.6.4 Sampling Forms 

Before leaving the monitoring site, all field forms, discharge measurement forms, and sample 

labels must be reviewed for legibility, accuracy, and completeness. Any changes in procedure 

due to field condition must be explained in the comments section. Make sure the information is 

complete on all forms. Record the departure time on the field form. After reviewing each form, 

initial the upper right corner of each page of the form. Document any photos taken by including 

the photo number on the field form. 

12.7 Handling and Custody

One part of proper data and sample handling procedures is to provide a complete record of the 

methods and procedures followed. Complete records are important to long-term monitoring so 

that anyone using the data may trace the sampling history. 

12.7.1 Field Data 

Field data will be collected on forms printed on waterproof paper. While at each monitoring site, 

the information recorded on the forms should include: 

• Date and day of week 

• Time of arrival 

• Names of field team members 

• GPS coordinates, to verify location 

• Current weather (air temperature and wind speed) and relevant notes about recent 

weather (storms or drought) 

• Observations of water quality conditions 

• Description of any photographs taken 

• Multiparameter sonde (model), calibration date, and field measurements of core suite 

variables 

• Sample identification numbers and collection times for advanced suite variables or 

quality assurance samples 

• Samples taken for laboratory analysis 

• Whether any samples were not collected, and reason 

• Flow discharge information and measurements (on separate form) 

• Any other required metadata for NPSTORET data entry 

• Time of departure 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 14 

All entries should be made clearly. If an incorrect entry is made, a single heavy line should be 

drawn through the incorrect entry and the correction made. All corrections should be initialed 

and dated. The completed field forms will be maintained in chronological order by station, 

copied into field binders and the originals maintained on file indefinitely. Field data are reviewed 

annually by network personnel (see SOP #8, Data Entry and Management, for details). 

12.7.2 Site/Sample Identity Codes 

Sampling stations will be identified by park, waterbody name, and river mile according to 

Network guidance. Information on the sampling station and park will comply with NPSTORET 

requirements. 

12.7.3 Data Transfer 

Enter field and laboratory data into NPSTORET as soon as possible after receiving the data, 

according to SOP #8. Field forms are the only written records of field measurements; place 

copies in field binders and keep originals on file indefinitely. Program sampling data and 

associated records are archived and stored in the GLKN Ashland Office. Boxes are numbered 

consecutively by year, project, and station number. 

Personnel entering data into the database should take care to enter laboratory data in consistent 

units. Different laboratories may report analytical results in different units (mg/L vs. μg/L) for 

the same analyte. Follow SOP #8, Data Entry and Management, when entering data. 

The contract laboratory should use the STORET-supported laboratory remark codes (Table 8) or 

provide a map relating their remark codes to these. Unlisted remark codes should be discussed 

for possible addition by the USEPA to the STORET codes. The detection descriptors to be used 

in data entry to STORET are listed in Table 9. 

12.7.4 Sample Transfer 

Conduct sample processing per SOP #7. Refrigerate or freeze samples, as required. Conduct inhouse laboratory work and package samples for sending to contract analytical laboratory. Sample 

preservation and conditions for shipment will differ for each parameter; these needs should be 

discussed ahead of time with the contract laboratory and documented. Fill out the analytical 

request form and chain-of-custody (COC) form provided by the laboratory (examples are 

included in SOP #7). The COC form is used to document the taking, shipment, and receipt of 

samples. The laboratory will use the COC to check samples into the analytical process. Clean all 

transfer bottles and equipment according to SOP #7. Water samples are maintained as close to 

sampling conditions as possible by shipping on ice. Chain-of-custody documentation will be 

maintained. A chain-of-custody includes not only the form, but all references to the sample in 

any form, document, or log book that allow tracing the sample back to its collection, and 

documents the possession of the samples from the time they were collected until the sample 

analytical results are received. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 15 

Table 8. STORET-supported laboratory remark codes. 

AL Aldol condensation present. Analyte may not be present. 

CNT Non-acceptable colony counts. 

EHT Sample or extract held beyond acceptable holding time. 

FBK Analyte found in blank. Sample contamination indicated. 

FDB Failed. Dry blank not acceptable. 

FDC Failed. Drift check not acceptable. 

FIS Failed. Internal standard not acceptable. 

FLD Failed. Lab duplicate not acceptable. 

FFD Failed. Field duplicate not acceptable. 

FFB Failed. Field blank not acceptable. 

FFS Failed. Field spike not acceptable. 

FFT Failed. Trip blank not acceptable. 

FLC Failed. Linearity check did not meet quality criterion. 

FLS Failed. Lab spike recovery not acceptable. 

FMS Failed. Matrix spike recovery not acceptable. 

FPC Failed. Lab performance check not acceptable. 

FQC Failed. Quality control criteria exceeded during analysis. 

FRS Failed. Internal reference sample not acceptable. 

FSP Failed. Surrogate spike recovery not acceptable. 

FSB Failed. Spiked field blank recovery not acceptable. 

FSL Failed. Spiked lab blank recovery not acceptable. 

INT Interference suspected. Analyte may not be present. 

ISP Improper sample preservation noted. Analysis performed. 

LIS Lab internal standard(s) added to sample. 

LLS Value less than lower quality control standard. 

PRE Presumptive evidence that analyte is present. 

NJ TIC, Tentatively Identified Compound, result is approximate 

N TIC, Tentatively Identified Compound, presumptive id only 

OUT Result value is defined as an outlier by data owner 

SUS Result value is defined as suspect by data owner 

Table 9. STORET detection descriptors. 

Detected and Quantified 

*Non-detect 

*Present > QL 

*Present < QL 

*Not Reported 

*Present 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 16 

12.8 Analytical Methods 

Field equipment and contract laboratories are likely to change during the course of this long-term 

monitoring project. Documentation will be maintained, therefore, as regards each multiprobe and 

contract laboratory’s ability to meet the data quality objectives of this project. Forms for this 

purpose are included in Attachment A. These completed forms for each multiprobe and contract 

laboratory will be maintained along with the maintenance logs for the multiprobe and QAPPs for 

each analytical laboratory. 

12.8.1 Field Methods 

One important aspect in the low uncertainty/bias and high precision of a water quality 

monitoring program is the correct selection probes for measuring field variable and their 

subsequent calibration and maintenance. Table 4 lists typical field sensor performance 

specifications that should be expected from monitoring equipment for this protocol. Table 10 

summarizes the ideal calibration frequency and minimum acceptance criteria for these sensor 

probes. The reality of logistical constraints at back country sites may preclude calibration and 

checks of calibration at the ideal frequency. 

Ensure calibration standards are not used beyond expiration dates. Refer to SOP #6 for an 

explanation of each parameter measured, guidelines on potential field measurement problems, 

and other details on performing calibration checks. Keep the manufacturer’s manual with each 

instrument for aid in troubleshooting. 

Used calibration solutions, in general, may be rinsed down a sink with water after consideration 

of the wastewater treatment system available to that sink. Material safety data sheets (MSDS), 

which are sent with manufacturer-purchased calibration solutions, should be kept on file. These 

documents describe the flammability, toxicity, and other safety hazards of reagents. Some 

reagents may include constituents toxic to aquatic life. These should not be rinsed down a sink in 

any large quantities in primitive areas where the ultimate destination of wastewater is the aquatic 

environment. These reagents should be collected in a leak-proof container that is properly 

marked, and disposed of in an adequate treatment system. 

Calibration logs for multi-parameter sondes will be maintained and will document the frequency 

of calibration and calibration checks. Data reporting units will be standardized by using the data 

sheet. Keep calibration and maintenance logs for multiparameter sondes with the sonde during 

the sampling season. Logs will later be archived at the Network office in Ashland, Wisconsin. A 

new log will be started for each field season. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 17 

Table 10. Field instrument ideal calibration frequencies and acceptance criteria. 

Parameter USEPA 

Method 

Minimum Calibration Frequency and 

QC checks 

Acceptance 

Criteria Corrective Actions 

Temperature 

thermometer 

or thermistor: 

170.1 Annually, 2-point check with NIST 

thermometer 

 

±1.0 oC 

Re-test with a different 

thermometer; repeat 

measurement 

Specific 

Conductance 

(SC25) 

120.1 Daily, prior to field mobilization; 

calibration check prior to each round 

of sampling 

10% of the readings taken each day 

must be duplicated or a minimum of 1 

reading if fewer than 10 samples are 

read. 

±5% 

RPD 10% 

Re-test; check low battery 

indicator; use a different 

meter; use different 

standards; repeat 

measurement 

pH 150.1 Daily, prior to field mobilization (two 

buffers should be selected that bracket 

the anticipated pH of the water body to 

be sampled with an independent third 

buffer selected to check instrument 

performance in that range); 

Calibration check w/ third buffer prior 

to each round of sampling 

10% of the readings taken each day 

must be duplicated or a minimum of 1 

reading if fewer than 10 samples are 

read. 

±0.05 pH unit 

±0.1 pH unit 

RPD 10% 

Re-test; check low battery 

indicator; use different 

standards; repeat 

measurement; don’t move 

cords or cause 

friction/static 

 

Dissolved 

Oxygen 

360.1 Daily, prior to field mobilization; 

check at the field site if elevation or 

barometric pressure changed since 

calibration 

0.2 mg/L 

concentration 

or 

±10% 

saturation 

Re-enter altitude; re-test; 

check low battery indicator; 

check membrane for 

wrinkles, tears or air 

bubbles; replace 

membrane; use a different 

meter; repeat measurement; 

allow more time for 

stabilization 

Depth -- Daily, prior to field mobilization, 

check at the field site. Check annually 

against commercially purchased brass 

sash chain labeled every 0.5 m to 

ensure that it reads zero at the surface 

and varies <0.3 m for depths <10 m 

and no more than 2% for greater 

depths. 

±0.1 m 

Retest, check low battery 

indicator; repeat 

measurement; use with 

accurately calibrated line 

Transparency 

tube 

-- Transparency tubes have a 100 or 120 

cm scale; ensure tube is clean 

±1.0 cm for 

transparency 

tube 

Clean tube with mild 

detergent and bottlebrush 

 

Marked lines 

(e.g., Secchi, 

Van Dorn) 

-- Check markings annually against brass 

sash chain. If lines are heated (for 

decontamination) check prior to each 

round of sampling. 

±1%, 0–10 m 

±2%, >10 m 

Re-mark line. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 18 

12.8.2 Field Equipment Performance Criteria 

The completeness, representativeness, precision, comparability, and systematic error of data 

generated by the use of a multiprobe will be estimated and documented according to this SOP. 

Data will be considered representative of the river when procedures detailed in the large rivers 

protocol narrative and associated SOPs are followed. Probabilistically chosen sites will confer 

some inference to larger areas than actually sampled, whereas judgementally chosen sites will 

not be considered representative of larger areas than those actually sampled. Actual sampling 

location and changes due to field conditions will be documented on the field forms. Data will be 

comparable year-to-year as objectives and methods chosen are consistent within documented 

NPS GLKN sampling procedures. 

12.8.2.1 Field Data Completeness 

The completeness of data collected, or percentage of intended field measurements that were 

actually made, will be calculated at year’s end according to the formula below. 

100

# _

# _ _ ×⎟

⎟

⎠

⎞

⎜

⎜

⎝

⎛ = samples planned

samples collected Percent completeness (1) 

12.8.2.2 Instrument Sensitivity 

Sensitivity of the multiprobe will be documented through an estimation of the limits of detection 

known as Alternative Measurement Sensitivity (AMS). The AMS for each multiprobe will be 

estimated annually, and for any new multiprobes, by taking multiple (at least 7) measurements in 

a field simulation for each parameter. Alternative Measurement Sensitivity (AMS) is a two-sided 

estimation based on the 99% confidence interval for sample size 7. Of interest is the size of the 

difference between two individual values that can be considered to actually be a true difference. 

This calculation differs from the MDL, which is a one-sided true difference from zero. The 

standard deviation will then be calculated and used in the estimation of AMS (3.708 x SD). This 

estimation will be carried out and documentation kept for a new probe and annually thereafter. A 

checklist (Attachment A) will be used for this documentation. Documentation will be kept in the 

project files. 

12.8.2.3 Instrument Precision 

The precision of the multiprobe will be estimated through the use of duplicates. Duplicates will 

be measured each day in the field at a rate of 10% (or 1 per park sampled if fewer than 10 sites 

are sampled). A reading will be considered a duplicate when it is repeated at a particular 

sampling site immediately after it is initially taken. Precision calculations are made by way of a 

Relative Percent Difference (RPD). Measurement Quality Objective (MQO) for precision: The 

RPD should be less than or equal to 10%; details and corrective actions are listed in Table 11. 

Calculate precision as follows, where A is the first reading and B is the second reading taken 

immediately after the first: 

( ) 100

/ 2

×⎟

⎟

⎠

⎞

⎜

⎜

⎝

⎛

+

− = A B

A B Precision (2) 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 19 

12.8.2.4 Instrument Bias 

The systematic error/bias of the multiprobe will be estimated through the use of reference 

solutions. Reference solutions will be measured prior to each round of sampling, in the lab or 

field. The results will be documented and used as a calibration check according to Table 10 as 

well as for a long-term estimate of systematic error/bias. Bias calculations are made by way of a 

Percent Difference (PD). Calculate bias as follows: 

⎟×100 ⎠

⎞ ⎜

⎝

⎛ − = X

Y X Bias (3) 

where X is the known (or expected) amount, and Y is the measured concentration. 

12.8.3 Laboratory 

The ability to use environmental data to reveal long-term trends requires consistent analytical 

methods and detection limits. The NPS recommendation is to use only laboratories with NELAC 

certification or at least certification by the state programs that also use the laboratory. The chosen 

contract laboratories must prove their capability annually through participation in blind quality 

control checks and other methods prescribed by the states in which they receive certification 

and/or federal programs in which they participate. Copies of certifications for each analyte 

and/or method will be kept on file along with Quality Assurance Project Plans (QAPPs) for each 

laboratory contracted for the duration of this monitoring effort. 

The method used in calculating method detection limits (MDLs) and method limit of quantitation 

(ML) or laboratory reporting limits (Lt-RL for USGS labs) may differ for each contract 

laboratory. Most laboratories routinely recalculate MDLs, MLs, and QC sample control limits 

using repeated measurement of standard samples or multiple percent recoveries on a quarterly or 

annual basis. The GLKN will request and maintain copies of this information as most recently 

calculated for the relevant analytical methods to assist in the selection of contract laboratories, 

data validation, and AMS calculations. 

A checklist to be used in selecting contract laboratories and documenting their compliance with 

GLKN QA/QC expectations is included in Attachment B. 

Great Lakes Network staff validating laboratory data for database entry should take care to 

ensure that data are entered in consistent units, as different laboratories may report results in 

different units (mg/L or μg/L) for the same analytes. A checklist to be used in data validation is 

included in Attachment B. 

12.8.4 Laboratory Performance Criteria 

Comparability, representativeness, precision, systematic error, and completeness of data 

generated by contract laboratories will be estimated and documented according to this SOP 

during data validation. Table 11 can be used as a guide. Unless otherwise justified (for example, 

to be consistent with State requirements), in no case will Measurement Quality Objectives less 

stringent than the following be accepted: 

• Precision - A maximum of 10% RPD for all lab parameters except chlorophyll-a, total 

suspended solids, and nutrients, for which the maximum RPD is 30% 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 20 

• Bias – A maximum of 15% PD for all parameters, or State credible data defaults, 

whichever is more stringent. 

All MQOs will be used as data rejection criteria. 

The data delivery package must contain QC sample results and an explanation of new STORET 

and NPSTORET compatible laboratory flags. A checklist to be used for documenting this 

procedure is included in Attachment B. 

Data generated will be considered representative of the particular site when samples are taken 

according to the sampling protocol for each sampling objective. Actual sampling location and 

changes due to field conditions will be documented on the field forms. Data will be comparable 

year-to-year as objectives and methods chosen are consistent within documented sampling 

procedures. 

12.8.4.1 Laboratory Data Completeness 

The completeness of data analyzed, or the percentage of intended sample measurements that 

were actually made, will be calculated at year’s end according to the formula below. Data points 

may be missed due to site conditions, sample container breakage, or disqualified analyses due to 

control limit exceedances in the laboratory. The reasons for missing data should be documented. 

100

# _

# _ _ ×⎟

⎟

⎠

⎞

⎜

⎜

⎝

⎛ = samples planned

samples analyzed Percent completeness (4) 

Determining required sample sizes and attendant completeness goals was done in a stepwise 

manner, considering desired statistical power and minimum detectable differences (see 

discussions in the protocol narrative). Should percent completeness ever fall below sample sizes 

needed for MDD and analysis of trends, adaptive changes will be made to ensure it does not 

happen again. 

12.8.4.2 Laboratory Sensitivity 

Measurement sensitivity is estimated in laboratory analysis through the use of signal to noise 

ratios or the standard deviation of repeat measurements of a low level reference standard. The 

method each laboratory uses to calculate MDLs and MLs will be documented using the data 

validation checklist. This information will be reviewed during data validation and kept along 

with other QA/QC information for each laboratory. 

12.8.4.3 Laboratory Precision 

Measurement precision and bias are estimated using a number of QC samples during a round of 

sample analysis for each method. A reference standard of a certified known concentration is 

analyzed along with samples at a rate specified by the laboratory’s QA/QC program. The results 

of these samples are reported and the percent difference calculated. Laboratory duplicates of 

field samples are also analyzed. This is a field sample that is split or subject to repeat analysis 

within the laboratory to estimate and control precision repeatability. Relative percent differences 

are calculated for laboratory duplicates. The percent difference and RPD of these QC samples 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 21 

should fall within the control limits specified by the laboratory (usually 10% to 20% depending 

on the type of analysis made). 

Field duplicates are to be sent to the analytical laboratory at a rate of at least one in every 10 

samples. A field duplicate is a sample co-located in time and space. The duplicate is usually 

given a separate sample identity on the sample label and forms, and it is noted on the field form 

for which sample this is a duplicate. This is a separate check on precision and repeatability of the 

laboratory analysis. The precision measurement is calculated using the Relative Percent 

Difference (RPD) between duplicate sample results per analyte. Precision estimates should be 

performed as soon as possible after receipt of laboratory results as part of data validation. 

Acceptance criteria and corrective actions are summarized in Table 11. 

Table 11 Frequency, acceptable range, and corrective actions for quality control (QC) samples. 

Type of QC 

Sample Frequency Acceptable Range for MQOs Corrective Action 

Field Duplicates

(samples) 

Minimum of 1 per trip 

per parameter or 10% 

of all samples per 

parameter per day 

All parameters ±15% 

RPD, chlorophyll-a, TSS 

and nutrients ± 30% 

Audit field personnel and verify sample 

collection procedure; resample; 

reanalyze; revise SOP; audit and train 

field personnel; project manager 

determines whether associated data is 

usable 

Field Duplicates

(multi-probes) 

Minimum of 1 per trip 

per parameter or 10% 

of all samples per 

parameter per day 

All parameters ±10% 

RPD 

Re-calibrate instrument; replace batteries; 

perform instrument field check with 

different standards; repair or replace 

instrument; notify management; audit and 

train field personnel; project manager 

determines whether 

Laboratory 

Control QC 

(bias) 

One each per 

analytical batch, 

minimum 1 per 20 

samples 

All parameters ± 15% 

RPD 

According to laboratory QAPP, ensure 

re-calibration, re-analysis and 

documentation. 

12.8.4.4 Laboratory Bias 

Systematic error/bias (formerly referred to as percent recovery) is estimated for each laboratory 

method through the analysis of spiked samples and/or certified reference materials. Spiked 

sample analyses are conducted by the contract laboratory to ensure the reported data are 

accurate, or compare favorably to the true values. A spiked sample consists of a sample with a 

known concentration of analyte added before any sample preparation procedures are carried out. 

Sample and spiked sample are analyzed using normal procedures and the percent spike 

difference is calculated. Percent difference is calculated as bias (equation 3, above). 

Other sources of systematic error in monitoring programs include sample cross contamination 

from field sampling equipment used to handle a multiple number of samples. Equipment blanks 

are used to estimate whether systematic error is added to sample data during sample handling. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 22 

The integrated sampler is to be rinsed in the field three times at each site prior to taking samples. 

Compositing jugs that are not site-dedicated may also be a source of cross contamination. Collect 

an equipment blank periodically, as follows: 

1. In between sample sites, rinse the equipment used to transfer water samples (integrating 

sampler or compositing jug) with laboratory reagent grade water three times and discard. 

2. Rinse with a fourth aliquot and save this aliquot to lab bottles as if it were a river sample 

to be analyzed. 

This sample is labeled equipment blank and information kept on a datasheet describing the 

source of the blank. Results for all parameters should be non-detect. This type of blank is a check 

for cross contamination between sampling sites and control for bias introduced by cross 

contamination. 

The laboratory QAPP should define control limits to be used during analysis of samples. If the 

analysis QC samples are not meeting the control limits, the analysis is usually repeated after recalibration. This protocol should be documented in the lab’s QAPP. During data validation 

GLKN will ensure that the laboratory performance meets the precision and bias MQOs tabulated 

in Table 11. 

12.8.5 Changing Methods and Documenting Cumulative Bias

When a field method is changed, the cumulative bias, or change in sampling results due to the 

method change alone, should be estimated. Cumulative bias can become significant over time 

even though changes in methods are small. When change occurs due to a scheduled change in 

staff, both the new staff member and old staff member should perform side-by-side field 

measurements several times (minimum of seven) during training when possible. The results for 

both will be compared as below. 

When purchasing a new probe, it should be used for a minimum of seven measurements side-byside with the existing probe when possible. 

When a change in laboratory methods is made by the laboratory, the laboratory will be 

responsible for estimating any bias introduced by the change. When a laboratory contract is 

changed to a different laboratory, a minimum of seven samples will be split for analysis in both 

labs. Data from these comparisons will be used to calculate a percent difference (PD) and 

fraction of change: 

⎟ ×100 ⎠

⎞ ⎜

⎝

⎛ − = old

new old PD (5) 

⎟

⎠

⎞ ⎜

⎝

⎛ = new

old Fraction _ (6) of _ change

where old = data from the older or original method and new = data from the new or replacement 

method. Ideally, the average PD (two-sided 95% t-distribution confidence interval) will be 

within 20% of the mean of the old or the new method measurements. If this is not the case, the 

number of overlapping measures should be increased until this criterion is met (Irwin 2006). 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 23 

New values can then be normalized to the old method value by multiplying them by the fraction 

of change. 

 Any bias should be stated clearly and documented. Documentation will be stored within each 

site file and should also include: 

• all raw data pairs for future use 

• standard deviation 

• the MDL or AMS of the method 

• number of paired samples 

• 95% t-distribution confidence interval for the measurement difference 

• dates between which overlapping measurements were made 

• date documentation calculation was made 

These comparisons of methods will be carried out, when possible, in order to document any bias 

that is introduced into the long-term data by a change in methodology and not in the actual 

environment. Due to the logistical realities imposed by sampling in remote locations and the 

reality of equipment loss or damage and abrupt changes in staff, this type of comparison may not 

always be possible. 

12.9 Instrument Calibration Frequency, Inspection, and 

Maintenance 

Instruments used in field measurement or laboratory analysis often require frequent inspection 

and maintenance to ensure they are in good working order. Calibration frequencies differ by 

instrument and should be spelled out in SOPs for both field and laboratory work to ensure 

consistency. 

12.9.1 Field Instruments 

Each instrument must have a logbook. The calibration schedule must be observed, using fresh 

calibration standards. Calibration solutions may be disposed of by rinsing down the work space 

sink if the contents do not include constituents that would harm the pipes or aquatic life on the 

receiving end of the available wastewater treatment (see relevant MSDS sheets). Calibration 

checks must be documented. 

When sensor probes are to be stored for extended periods of time, thoroughly clean sensors, 

remove batteries, and store sonde according to specific instructions in SOP #11 and 

manufacturer’s manual. Store calibration standards and electrolyte solutions in a temperaturecontrolled environment. 

12.9.2 Laboratory Instruments 

Instrument calibration and verification is performed at least once a day for each analytical 

method prior to the analysis of samples. Each laboratory specifies its own procedure, which 

should include multiple point calibrations plus a blank, continuing calibration verification, and 

final calibration verification at the end of an analytical run. Each laboratory should define the 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 24 

procedures in a QAPP. Review of these procedures will be documented using the laboratory 

checklist in Attachment B. 

12.10 Inspection and Acceptance of Supplies and 

Consumables 

Monitoring water quality requires many pieces of equipment and a large amount of supplies. 

Table 12 lists the SOPs that include checklists of supplies and equipment. When new equipment 

is received or equipment is returned after repair, inspect it for flaws and test it to ensure proper 

functioning. When supplies are received, inspect them to ensure containers are properly sealed. 

Ensure reagent containers are dated upon receipt and upon opening. Commercially purchased 

calibration standards come with an expiration date that must be observed. 

Table 12. Checklists of equipment and supplies for monitoring water quality of large rivers. 

Checklist Location 

Safety equipment and supplies SOP #2 

Decontamination equipment and supplies SOP #5 

Field equipment and supplies SOP #6 

Laboratory equipment and supplies SOP #7 

12.11 Records Management

All records must be kept, from field activity through sample results. Required metadata will be 

complete. Table 13 summarizes the QA/QC procedures related to data management. For more 

details on the Great Lakes Network’s overall strategy for metadata generation, management, and 

distribution see chapter 8, Data Documentation, of GLKN’s Data Management Plan (Hart and 

Gafvert 2005) and the appendices of that document. 

Data will be archived according to SOP #8 (Data Entry and Management) for digital data, paper 

copies, and field forms. Field forms are maintained indefinitely. Brief characterizations of the 

data from each NPS unit that was sampled and the Network as a whole will be performed each 

year, after all QA/QC procedures have been completed. For each station sampled, these 

descriptive statistics will include mean, median, maximum and minimum values, skew, kurtosis, 

and measures of variability (e.g., CV, standard error, variance) for each water quality variable. 

Understanding of landscape-scale dynamics will be provided by analyses of variability among 

stations within the domain of interest (e.g., upper St. Croix River), following one of several 

approaches described in SOP #9, Data Analysis. 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 25 

Table 13. Summary of QA/QC procedures pertaining to data management. 

Procedure Description 

Instrument calibration logs Each instrument must have a logbook. 

Field forms 

Field forms are the only written record of field measurements. 

Place copies in site binders and keep originals on file 

indefinitely. 

Estimating precision 

The precision measurement is calculated using the Relative 

Percent Difference (RPD) between duplicate sample results per 

analyte. Precision estimates should be performed within 7 days 

of receipt of laboratory results. 

Electronic data entry 

Approximately 10% of electronic data entries should be spot 

checked for errors on a random basis. If errors are found, 

another 10% are spot checked. 

Data archiving 

Sampling data and associated records are archived in boxes 

and stored at the GLKN Ashland office. Boxes are numbered 

consecutively by year, project, and station number. 

Data validation Data validation is the process that determines whether quality 

control objectives for data collection were met. 

Data validation reports 

Data validation reports provide a narrative that discusses any 

deviations from QA/QC procedures and the impacts of those 

deviations. 

Data verification Data verification demonstrates that a data set will qualify as 

credible data. 

Data verification reports Data verification reports document the results of the data 

verification procedure. 

Data qualification codes Data must be fully qualified before uploading to the Water 

Resources Division’s NPSTORET 

12.12 Assessment and Oversight 

It is the project manager’s responsibility to make sure each component of this and other SOPs are 

followed. 

12.12.1 Corrective Responsive Actions

The project manager, in consultation with experienced professionals, will be responsible for 

taking corrective responsive action in the case in which QA/QC is not followed or in the case of 

an unexpected event. Responsive action is often needed in the event of broken sample bottles, 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 26 

missing data, errors on field sheets, changes due to field conditions, problematic analyses, and 

other events that do not fall within the standard operating procedures. A “Memo-to-file” will be 

used to document any decisions or corrections that are made. This memo will include the date, 

name of author, site or sample referred to, a description of the problem or error and a statement 

describing the decision made or action taken. The memo will be archived with the appropriate 

site data and files. 

12.13 Reports to Management

Routine data summaries will occur annually for areas that are sampled within that year, and 

annual summary reports will be produced, with the primary audience being the parks. These 

reports will be provided to parks and partners as soon as possible following the sampling season. 

More comprehensive analyses of trends will occur for most parameters after three or more years 

of sampling. For stations that are located where no previous monitoring has occurred, this period 

of time is the minimum needed to establish a time series sufficiently powerful to detect 

meaningful levels of change (e.g., 20%) through time. The target audience of the analysis and 

synthesis reports will be the parks, the Network, both regional and Servicewide I&M, and the 

broader scientific community. Drafts will be reviewed internally and sent to the parks, and 

possibly outside sources, for further review. The extent of review will depend on how 

analytically complicated the methods are and the gravity of inference and recommendations. 

12.14 Data Validation and Usability

Data validation is the method in which data are proven or disproved to be accurate. This process 

involves the review of the results of all measurements, samples, and QC samples. Field data 

sheets and laboratory data are reviewed for transcription errors, completeness, verification of 

calibration and quality control check samples or standards. 

A checklist for use in data validation is presented in Attachment B. Data are validated by 

comparing the actual estimates for MDL and ML, precision, bias/uncertainty for each analytical 

run to the expected quality of results. Once this information is documented, the decision is made 

by the project manager on the usability of the data. Data may be flagged as between MDL and 

ML and therefore highly uncertain (J). Data may be flagged (B) if the analyte was detected in the 

blank at a concentration similar to that in the sample (laboratory flagging rules may differ 

slightly). These types of flagged data contain much more uncertainty than unflagged data. The 

decision must be made whether or not to add them to the database or merely maintain them in 

files for future reference. Some investigation into the sampling method or laboratory method 

may be needed if ‘B’ flagged data are a continual occurrence or if the required MLs are 

repeatedly unmet. 

NPSTORET itself includes some form-based QA/QC tests on data entry. The system does not 

allow entry of results below the ML but will flag the data as “present, not quantified”. The 

project manager, in consultation with other NPS or outside experts, will flag data when they fall 

outside of expected limits. Laboratory results below detection limits (ND) will be kept in the 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 27 

archives as ‘ND’ and will be handled statistically according to recent literature (e.g., Helsel 

2005) in summary and analysis reports. 

12.15 Reconciliation with Data Quality Objectives

Once data validation is complete, the project manager then calculates percent completeness, 

compares the results to the data quality objectives, and determines whether or not the data meet 

the objectives for both the field and laboratory components of the project. 

12.16 Literature Cited

Hart, M., and U. Gafvert. 2005. Data management plan: Great Lakes Inventory & Monitoring 

Network (draft). National Park Service Great Lakes Inventory and Monitoring Network 

GLKN/2005/20. 

Helsel, D.R. 2005. Nondetects and data analysis: statistics for censored environmental data 

(statistics in practice). John Wiley & Sons, New York. 

Irwin, R.J. 2006. Draft Part B lite (Just the Basics) QA/QC Review Checklist for Aquatic Vital 

Sign Monitoring Protocols and SOPs, 62 pp., National Park Service, Water Resources 

Division. Fort Collins, Colorado, distributed on Internet only at 

http://www.nature.nps.gov/water/Vital_Signs_Guidance/Guidance_Documents/part_b_lit

e_05_2005.pdf

Irwin, R. 2004. Part B: Planning process steps. Issues to consider and then to document in a 

detailed study plan that includes a quality assurance project plan (QAPP) and monitoring 

protocols (standard operating procedures). National Park Service, Ft. Collins, Colorado. 

available at http://science.nature.nps.gov/im/monitor/protocols/wqPartB.doc

Ledder, T. 2003. Water resource information and assessment report for the Great Lakes 

Inventory and Monitoring Network. National Park Service, Great Lakes Inventory and 

Monitoring Network, Ashland, Wisconsin. Great Lakes Network Technical Report: 

GLKN/2003/05. 

MDEQ. 2005. Michigan Department of Environmental Quality Environmental & Drinking 

Water Testing Labs Directory. http://www.michigan.gov/deq/0,1607,7-135-6132_6828-

18205--,00.html

MDH. 2005. Minnesota Department of Environmental Health Laboratory Certification Program. 

http://www.health.state.mn.us/divs/phl/cert/index.html

NEMI. 2006. National Environmental Methods Index website as accessed during the 

 month of July, 2006. http://www.nemi.gov 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 28 

NPS (National Park Service). 1999. Baseline water quality data inventory and analysis: Apostle 

Islands National Lakeshore. National Park Service, Water Resources Division. Fort 

Collins, Colorado. Technical Report NPS/NRWRD/NRTR-98/188. 

NPS (National Park Service). 1995a. Baseline water quality data inventory and analysis: Isle 

Royale National Park. National Park Service, Water Resources Division. Fort Collins, 

Colorado. Technical Report NPS/NRWRD/NRTR-95/41. 

NPS (National Park Service). 1995b. Baseline water quality data inventory and analysis: 

Mississippi River National River and Recreation Area. National Park Service, Water 

Resources Division. Fort Collins, Colorado. Technical Report NPS/NRWRD/NRTR95/61. 

NPS (National Park Service). 1995c. Baseline water quality data inventory and analysis: Saint 

Croix National Scenic Riverway. National Park Service, Water Resources Division. Fort 

Collins, Colorado. Technical Report NPS/NRWRD/NRTR-95/69. 

O’Ney, S.E. 2005. Regulatory water quality monitoring protocol. Version 1.0. National Park 

Service, Greater Yellowstone Network, Bozeman, Montana. See: 

http://science.nature.nps.gov/im/monitor/protocoldb.cfm

USEPA. 2000. Ecoregional Nutrient Criteria as accessed on June 2, 2006 at 

www.epa.gov/waterscience/criteria/nutrients/ecoregion/sumtable.pdf

USGS (US Geological Survey). 2003. Evaluation of alkaline persulfate digestion as an 

alternative to Kjeldahl digestion for determination of total and dissolved nitrogen and 

phosphorus in water, by Charles J. Patton and Jennifer R. Kryskalla. U.S. Geological 

Survey Water-Resources Investigations Report 03-4174. 

WOW. 2005. Water on the Web - Monitoring Minnesota lakes on the internet and training water 

science technicians for the future - a national on-line curriculum using advanced 

technologies and real-time data. (http://waterontheweb.org). 

WSLH. 2003. Wisconsin State Laboratory of Hygiene, Environmental Health Division 

Analytical Services and Methods. University of Wisconsin, Madison, Wisconsin. 

http://www.slh.wisc.edu/services/index.php 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 29 

Attachment A 

Checklists for: 

Analytical Methods 

Selection of Multiprobe 

Selection of Laboratory 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 30 

Multiprobe Checklist 

Probe ____________________________ Purchased __________________________ 

Serial Number_____________________ Location used _______________________ 

Manufacturer’s Stated Limits 

Sensor Range Reporting 

Resolution Bias Stabilization Criteria 

Temperature 

Sp. Cond. 

(SC25) 

pH 

DO (Conc.) 

DO (% sat.) 

Depth – Z 

(pressure 

sensor) 

 

Alternative measurement sensitivity by multiple field readings 

Location ______________________ Performed by_____________________ 

Date _______________ Began calibration log _____ 

Sensor 1 2 3 4 5 6 7 

Temperature 

Specific 

Conductivity 

(SC25) 

 

 

pH 

(sensor units) 

DO (Conc.) 

DO (% sat.) 

Depth – Z 

(pressure 

sensor) 

 

 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 31 

Calculations 

For each parameter calculate the standard deviation of the 7 readings. 

Sensor Standard 

deviation 

AMS 

3.708x sd

Temperature 

Specific 

Conductivity 

(SC25) 

 

pH 

(sensor units) 

 

DO (Conc.) 

DO (% sat.) 

Depth – Z 

(pressure 

sensor) 

 

Alternate Measurement Sensitivity is a two-sided estimation based on the 99% confidence interval for 

sample size 7. Of interest is the size of the difference between two individual values that can be 

considered to actually be a true difference. The MDL is a one-sided true difference from zero.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 32 

Contract Laboratory Checklist 

Laboratory 

Address 

Contact person 

_____ Received QAPP 

_____ Received copy of certifications 

_____ Received a list of analytical methods used 

_____ Define the limits of detection and limit of quantitation calculation method 

 (can lab report as MDL and ML if currently calculated as LOD and LOQ?) 

_____ Received a copy of latest MDL/ML/control limits calculations for relevant methods 

_____ MDL/ML as listed meet project needs 

 (list any analyte for which the ML requirement is not met – discuss options with lab) 

_____ Received successful interlaboratory participation documentation 

_____ Sample handling log in and COC are documented in the QAPP 

_____ Equipment maintenance and calibration procedures are documented in the QAPP 

_____ Internal QA/QC documented in QAPP 

Control limits calculations are made by what method 

 (QC includes blanks, duplicates, spikes, reference standards and LCS) 

Calibration curves cover level of analytical interest 

 (QC includes ICV and ICB, and CCV and CCB) 

Reporting data flags used include 

Attach all copies 

Reviewed by ________________________________________ Date _____________ 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 33 

Attachment B 

Checklists for data validation 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 34 

Field Measurement Validation Checklist

(one sheet per park sampled) 

Sampling Unit _________________ 

Date Sampled __________________ 

Date Reviewed _________________ 

Reviewed by ___________________ 

____________ All field forms have been received (data sheet, flow, etc.) 

____________ Multiprobe was calibrated correctly 

____________ Multiprobe post-calibration checks were successful 

____________ Field duplicates were within range 

____________ Multiprobe end of use calibration checks were successful 

____________ There were no obvious trends in data taken from any sensor during the sampling 

day 

____________ Equipment blanks sent to lab included 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page 35 

Laboratory Data Validation Checklist 

Sample set from_____________ 

Date taken ________________ 

Received data ______________ 

Reviewed by _______________ 

Review date _________________ 

_____ Samples received by lab at proper temperature (look at COC copy from lab) 

_____ Holding time limits met 

_____ Analytical methods used in analyses were those agreed upon 

_____ Useable MDL and ML achieved in this analytical run 

_____ Calibration procedures were followed 

QC samples control limits applicable to this analytical batch 

 Lab blank _____ 

 Lab dup _____ 

 Lab LCS _____ 

 Lab spikes _____ 

 Field dup _____ 

 Eq blank _____ 

 CCVs _____ 

QC samples within range expected 

 Lab blank _____ 

 Lab dup _____ 

 Lab LCS _____ 

 Lab spikes _____ 

 Field dup _____ 

 Eq blank _____ 

 CCVs _____ 

Lab notes or flags 

Samples rejected 

Signature of Reviewer ______________________________________________ 
Standard Operating Procedure #13: 

Revising the Protocol 

Version 1.0 

In Large Rivers Water Quality Monitoring Protocol 

Prepared by 

Suzanne Sanders and Joan Elias 

National Park Service 

Great Lakes Inventory and Monitoring Network 

2800 Lake Shore Drive East 

Ashland, Wisconsin 54806 

joan_elias@nps.gov 

 

August 2008 

Suggested citation: Sanders, S., and J. Elias. 2008. Standard operating procedure #13: Revising 

the protocol. in Magdalene S., D.R. Engstrom, and J. Elias. 2008. Large rivers water quality 

monitoring protocol, Version 1.0. National Park Service, Great Lakes Network, Ashland, 

Wisconsin. NPS/GLKN/NRR—2008/060. National Park Service, Fort Collins, Colorado.
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #13, page ii 

Contents 

 Page

Revision History Log.................................................................................................................... iii 

13.0 Introduction.........................................................................................................................1 

13.1 Steps for Revising the Protocol...........................................................................................1 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #12, page iii 

Revision History Log 

 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project leader and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file.

Revision History Log: 

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Large Rivers Water Quality Monitoring Protocol, Version 1.0 August 2008 

SOP #13, page 1 

13.0 Introduction

Because of the long-term nature of the National Park Service’s monitoring program, the projects 

must necessarily accommodate change. Refined field methods, advances in analysis techniques, 

and feedback from field crews and project managers can all contribute to improving the 

monitoring protocol. The purpose of this SOP is to define a systematic and routine process for 

incorporating these changes into the protocol. 

13.1 Steps for Revising the Protocol 

1. Attempt to incorporate any needed changes by first modifying only the SOP(s), without 

making changes to the protocol narrative. However, if it is clear that changes will also be needed 

to the narrative, then revise it as well. 

2. Make all revisions using the Track Changes feature of Microsoft Word. For minor changes, at 

least one other person must review the revision. If the change is more extensive, a discussion of 

the changes by Network staff is warranted before acceptance of the revision. For major changes, 

review from outside of the Network should be sought. Examples of major changes include 

modifications of the sampling design, substantially altered field methods, and revised analysis 

techniques. 

3. Record the changes in the revision history log of the SOP and/or in the narrative, as 

appropriate. Include the date of revision, full name(s) and affiliation(s) of the previous author(s), 

description of and reasons for the changes, and section of SOP or narrative where changes were 

made. 

4. Rename the version of the SOP and/or narrative. For minor changes, only revise the version 

number after the decimal point (e.g., change Version 1.1 to Version 1.2). For major changes, 

revise the number before the decimal point (e.g., Version 2.3 to 3.0). Also change the version 

number of the SOP or protocol in the header or footer, as appropriate. 

5. Notify the data manager of the change(s) so that the metadata of the project database will be 

updated. 

6. Distribute the revised version to all appropriate parties, including the members of the field 

crew and appropriate GLKN staff. The revised version must also be posted on the Network’s 

website. 

7. Maintain a library of previous versions. Such historical information may be crucial for 

understanding, interpreting, and analyzing data. 
The Department of the Interior protects and manages the nation’s natural resources and cultural heritage; provides scientific and 

other information about those resources; and honors its special responsibilities to American Indians, Alaska Natives, and 

affiliated Island Communities. 

NPS D-82, August 2008 
National Park Service 

U.S. Department of the Interior 

 

Natural Resource Program Center 

1201 Oak Ridge Drive, Suite 150 

Fort Collins, CO 80525 

www.nature.nps.gov 

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