Long Term Resource Monitoring Program

Technical Report 

2004-T002-01

March 2004

Long Term Resource Monitoring Program Procedures:

Water Quality Monitoring
Long Term Resource Monitoring Program Technical Reports

provide Long Term Resource Monitoring Program 

partners with scientific and technical support.

All reports in this series receive anonymous peer review.

 

Cover graphic by Mi Ae Lipe-Butterbrodt

Mention of trade names or commercial products does not constitute endorsement

or recommendation for use by the U.S. Department of the Interior, U.S. Geological Survey.
Long Term Resource Monitoring Program Procedures: 

Water Quality Monitoring

by

David M. Soballe1 

U.S. Geological Survey

Upper Midwest Environmental Sciences Center

2630 Fanta Reed Road

La Crosse, Wisconsin 54603

James R. Fischer2 

Wisconsin Department of Natural Resources

575 Lester Avenue

Onalaska, Wisconsin 54650

March 2004

1

Present address: Engineer Research and Development Center, Vicksburg, Mississippi 39180

2

Present address: 2630 Fanta Reed Road, La Cosse, Wisconsin 54603
Suggested citation:

Soballe, D. M., and J. R. Fischer. 2004. Long Term Resource Monitoring Program Procedures: Water quality monitoring. 

U.S. Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, Wisconsin, March 2004. 

Technical Report LTRMP 2004-T002-1 (Ref. 95-P002-5). 73 pp. + Appendixes A–J
iii

Preface

The Long Term Resource Monitoring Program (LTRMP) was authorized under the Water Resources Development Act of 1986 (Public Law 99-662) as an element of the U.S. Army Corps of 

Engineers’ Environmental Management Program. The LTRMP is being implemented by the Upper 

Midwest Environmental Sciences Center, a U.S. Geological Survey science center, in cooperation 

with the five Upper Mississippi River System (UMRS) States of Illinois, Iowa, Minnesota, Missouri, 

and Wisconsin. The U.S. Army Corps of Engineers provides guidance and has overall Program responsibility. The mode of operation and respective roles of the agencies are outlined in a 1988 Memorandum of Agreement.

The UMRS encompasses the commercially navigable reaches of the Upper Mississippi River, as 

well as the Illinois River and navigable portions of the Kaskaskia, Black, St. Croix, and Minnesota 

Rivers. Congress has declared the UMRS to be both a nationally significant ecosystem and a nationally significant commercial navigation system. The mission of the LTRMP is to provide decision 

makers with information for maintaining the UMRS as a sustainable large river ecosystem given its 

multiple-use character. The long-term goals of the Program are to understand the system, determine 

resource trends and effects, develop management alternatives, manage information, and develop useful products.

This report was prepared under Strategy 2.2.3, Monitor and Evaluate Water Quality, of the Operating Plan (U.S. Fish and Wildlife Service 1993). This report was developed with funding provided by 

the LTRMP.
iv
v

 Page

Preface ....................................................................................................................................................iii

1. Rationale and Strategy for Monitoring Water Quality............................................................................. 1

 1.1 General Sampling Approach ............................................................................................................. 2

 1.1.1 Fixed-Site Sampling Design ........................................................................................................ 2

 1.1.2 Stratified Random Sampling Design ........................................................................................... 3

 1.1.2.1 Definition of Sampling Strata ............................................................................................... 4

 1.1.2.2 Changes in Stratum Boundaries ............................................................................................ 4

 1.1.2.3 Atypical Conditions within Strata ......................................................................................... 4

 1.1.2.4 Changes in the River Over Time ........................................................................................... 4

 1.1.2.5 Remapping of Sampling Strata ............................................................................................. 5

 1.1.2.6 Spatial-Temporal Scales and Cross-Component Consistency .............................................. 5

 1.1.3 Other Sampling Approaches ........................................................................................................ 5

 1.2 Sampling Schedule ............................................................................................................................ 6

 1.3 Standardization and Randomization of Sampling Time .................................................................... 6

 1.4 Geographic Coordinates .................................................................................................................... 6

 1.5 Fixed-site Sampling Locations .......................................................................................................... 7

 1.5.1 Main Stem Location Codes ......................................................................................................... 7

 1.5.2 Tributary Location Codes ............................................................................................................ 7

 1.6 Stratified Random Sampling Locations ............................................................................................. 8

 1.7 Locating Stratified Random Sampling Locations in the Field ......................................................... 10

 1.8 Use of Alternate Sites in Stratified Random Sampling ................................................................... 10

 1.8.1 Requirement to Sample an Alternate Site ................................................................................. 10

 1.8.2 Picking an Alternate Site ........................................................................................................... 11

 1.8.3 Limits on the Replacement of Primary Sites with Alternates ................................................... 11

 1.9 Site Location Maps .......................................................................................................................... 12

2. Quality Assurance and Quality Control (QA/QC)................................................................................. 12

 2.1 QA/QC Samples for Chemical Constituents ................................................................................... 12

 2.1.1 QA/QC Sampling Types ............................................................................................................ 14

 2.1.2 Selection of Sampling Sites for QA/QC Measurements ........................................................... 14

 2.1.3 Incomplete QA/QC .................................................................................................................... 16

 2.1.4 Collection and Processing of QA/QC Samples and Measurements .......................................... 16

 2.2 Equipment Calibration ..................................................................................................................... 17

 2.3 Quality Factor Codes ....................................................................................................................... 18

3. Sampling Site Characteristics and Conditions....................................................................................... 18

 3.1 Water Depth ..................................................................................................................................... 18

 3.1.1 Definition ................................................................................................................................... 18

 3.1.2 Method ....................................................................................................................................... 19

 3.2 Water Depth—Available .................................................................................................................. 19

 3.2.1 Definition ................................................................................................................................... 19

 3.2.2 Method ....................................................................................................................................... 19

 3.3 Water Elevation ................................................................................................................................ 19

 3.4 Wave Height .................................................................................................................................... 20

 3.4.1 Definition ................................................................................................................................... 20

 3.4.2 Method ....................................................................................................................................... 20

 3.5 Water Current Velocity .................................................................................................................... 20

Contents
vi

 3.5.1 Definition ................................................................................................................................... 21

 3.5.2 Method ....................................................................................................................................... 21

 3.6 Water Current Velocity Category .................................................................................................... 22

 3.7 Water Current Direction ................................................................................................................. 22

 3.7.1 Definition ................................................................................................................................... 22

 3.7.2 Method ....................................................................................................................................... 22

 3.8 Ice and Snow .................................................................................................................................... 22

 3.8.1 Ice—Percent Cover ................................................................................................................... 23

 3.8.1.1 Definition ............................................................................................................................ 23

 3.8.1.2 Method ................................................................................................................................ 23

 3.8.2 Ice—Total Thickness ................................................................................................................. 23

 3.8.2.1 Definition ............................................................................................................................ 23

 3.8.2.2 Method ................................................................................................................................ 23

 3.8.3 Ice—Submerged Thickness ....................................................................................................... 24

 3.8.3.1 Definition ............................................................................................................................ 24

 3.8.3.2 Method ................................................................................................................................ 24

 3.8.4 Snow Depth ............................................................................................................................... 24

 3.8.4.1 Definition ............................................................................................................................. 24

 3.8.4.2 Method ................................................................................................................................. 24

 3.8.5 Snow—Percent Cover ............................................................................................................... 24

 3.8.5.1 Definition ............................................................................................................................. 24

 3.8.5.2 Method ................................................................................................................................. 24

 3.9 Substrate Characteristics .................................................................................................................. 25

 3.9.1 Substrate Particle Size ............................................................................................................... 25

 3.9.1.1 Method ................................................................................................................................. 25

 3.9.2 Substrate Hardness .................................................................................................................... 25

 3.9.2.1 Method ................................................................................................................................. 26

 3.9.3 Predominant Substrate ............................................................................................................... 26

 3.10 Aquatic Vegetation ......................................................................................................................... 26

 3.10.1 Percent Aquatic Plant Coverage .............................................................................................. 26

 3.10.2 Vegetation Density .................................................................................................................. 27

 3.10.3 Vegetation Type ....................................................................................................................... 27

4. Physical and Aggregate Properties of Water.......................................................................................... 27

 4.1 Conductivity .................................................................................................................................... 27

 4.1.1 Definition ................................................................................................................................... 27

 4.1.2 Method ....................................................................................................................................... 28

 4.2 pH ..................................................................................................................................................... 28

 4.2.1 Definition ................................................................................................................................... 28

 4.2.2 Method ....................................................................................................................................... 28

 4.3 Photosynthetically Active Radiation ............................................................................................... 28

 4.3.1 Definition ................................................................................................................................... 28

 4.3.2 Method ....................................................................................................................................... 29

 4.4 Secchi Disk Transparency ............................................................................................................... 29

 4.4.1 Definition ................................................................................................................................... 29

 4.4.2 Method ....................................................................................................................................... 29

 4.4.3 Calibration ................................................................................................................................. 30

 Page
vii

 4.5 Suspended Solids ............................................................................................................................. 30

 4.5.1 Definition ................................................................................................................................... 31

 4.5.2 Method ....................................................................................................................................... 31

 4.6 Temperature—Water ........................................................................................................................ 32

 4.6.1 Definition ................................................................................................................................... 33

 4.6.2 Method ....................................................................................................................................... 33

 4.7 Turbidity .......................................................................................................................................... 33

 4.7.1 Definition ................................................................................................................................... 34

 4.7.2 Method ....................................................................................................................................... 34

 4.8 Vertical Density Stratification .......................................................................................................... 36

 4.8.1 Definition ................................................................................................................................... 36

 4.8.2 Method ....................................................................................................................................... 36

5. Concentration of Chemical Constituents............................................................................................... 36

 5.1 Chloride ........................................................................................................................................... 37

 5.1.1 Definition ................................................................................................................................... 37

 5.1.2 Sample Collection and Preservation .......................................................................................... 37

 5.2 Metal Cations (Calcium, Iron, Magnesium, Manganese, Potassium, and Sodium) ........................ 37

 5.2.1 Definition ................................................................................................................................... 37

 5.2.2 Sample Collection and Preservation .......................................................................................... 38

 5.3 Nitrogen—Ammonia plus Ammonium ........................................................................................... 38

 5.3.1 Definition ................................................................................................................................... 38

 5.3.2 Sample Collection and Preservation .......................................................................................... 38

 5.4 Nitrogen—Nitrate Plus Nitrite ......................................................................................................... 38

 5.4.1 Definition ................................................................................................................................... 38

 5.4.2 Sample Collection and Preservation .......................................................................................... 39

 5.5 Nitrogen—Total ............................................................................................................................... 39

 5.5.1 Definition ................................................................................................................................... 39

 5.5.2 Sample Collection and Preservation .......................................................................................... 39

 5.6 Oxygen—Dissolved ......................................................................................................................... 39

 5.6.1 Definition ................................................................................................................................... 40

 5.6.2 Method ....................................................................................................................................... 40

 5.6.3 General Guidelines .................................................................................................................... 40

 5.7 Phosphorus—Soluble Reactive ....................................................................................................... 41

 5.7.1 Definition ................................................................................................................................... 41

 5.7.2 Sample Collection and Preservation .......................................................................................... 41

 5.8 Phosphorus—Total .......................................................................................................................... 42

 5.8.1 Definition ................................................................................................................................... 42

 5.8.2 Sample Collection and Preservation .......................................................................................... 42

 5.9 Silica—Dissolved ............................................................................................................................ 42

 5.9.1 Definition ................................................................................................................................... 42

 5.9.2 Sample Collection and Preservation .......................................................................................... 42

 5.10 Sulfate—Dissolved ........................................................................................................................ 42

 5.10.1 Definition ................................................................................................................................. 42

 5.10.2 Sample Collection and Preservation ........................................................................................ 43

6. Biological Measurements....................................................................................................................... 43

 6.1 Phytopigments (Chlorophyll-a and Phaeophytin) ........................................................................... 43

 Page
viii

 6.1.1 Definition ................................................................................................................................... 43

 6.1.2 Sample Collection and Preservation .......................................................................................... 44

 6.1.2.1 Method—Spectrophotometric Chlorophyll FIltration ........................................................ 44

 6.1.2.2 Method—Spectrophotometric Chlorophyll-a FIltration ..................................................... 45

 6.2 Phytoplankton .................................................................................................................................. 46

 6.2.1 Definition ................................................................................................................................... 46

 6.2.2 Sample Collection and Preservation .......................................................................................... 46

 6.3 Zooplankton ..................................................................................................................................... 46

 6.3.1 Definition ................................................................................................................................... 46

 6.3.2 Sample Collection and Preservation .......................................................................................... 46

7. Field Sampling of Physical and Chemical Water Characteristics.......................................................... 46

 7.1 Sampling Site Inaccessible or Unusable .......................................................................................... 47

 7.2 Shallow Water Sampling ................................................................................................................. 47

 7.3 Discrete-Depth Sampling ................................................................................................................ 48

 7.4 Subsurface Sampling Requirements ................................................................................................ 48

 7.5 Sampling During Ice Cover ............................................................................................................. 49

 7.5.1 Suitability for SRS Sampling .................................................................................................... 49

 7.5.2 Sampling Requirements with Ice Cover .................................................................................... 49

 7.5.3 Ice Extends to Substrate ............................................................................................................ 50

 7.5.4 Unconsolidated Ice .................................................................................................................... 50

 7.5.5 Ice Surface Submerged .............................................................................................................. 50

 7.6 Chemical Sampling when Dissolved Oxygen is Less Than 1 mg/L ............................................... 50

 7.7 Selecting Sites for Chlorophyll-a Calibration and QA/QC ............................................................. 51

 7.7.1 Method ....................................................................................................................................... 51

 7.8 Sample Preparation For Shipment and Analysis ............................................................................. 51

 7.8.1 Sample Treatments..................................................................................................................... 52

 7.8.2 Filtration of Inorganic Chemical Samples ................................................................................. 53

 7.8.3 Acid Preservation of Samples ................................................................................................... 53

 7.8.4 Filling of Sample Bottles: Rinsing and Agitation ...................................................................... 55

 7.8.5 Filtration Using a Peristaltic Pump ............................................................................................ 55

 7.8.6 Freezing of Samples for Preservation ........................................................................................ 56

 7.9 Holding Times For Storage and Shipment of Chemical Samples ................................................... 56

 7.10 Sample Containers: Size, Composition, and Integrity ................................................................... 56

 7.11 Quality of Water for Cleaning and Sample Preparation ................................................................ 57

 7.12 Cleaning of Sample Containers ..................................................................................................... 57

 7.13 Cleaning of Sampling Devices and Tubing ................................................................................... 58

 7.14 Bar Code Labeling of Samples and Data Sheets ........................................................................... 58

 7.15 Sample Submission Procedures ..................................................................................................... 59

 7.15.1 Scanning Samples for Custody Tracking and Shipment ......................................................... 59

 7.15.2 Packaging Samples for Shipment ............................................................................................ 60

8. Field Data Recording and Reporting ..................................................................................................... 60

 8.1 Sample Batches ................................................................................................................................ 62

 8.2 Crew Leader and Recorder Codes ................................................................................................... 62

 8.3 Data Sheet Description .................................................................................................................... 62

 8.4 Use of Quality Factor Codes ............................................................................................................ 62

 8.5 Data Sheet Submission .................................................................................................................... 69

 Page
ix

 8.6 Electronic Data Acquisition ............................................................................................................. 69

 8.7 Archival Storage of Data and Associated Records .......................................................................... 70

9. Acknowledgment ................................................................................................................................... 71

10. References............................................................................................................................................ 71

11. Glossary ............................................................................................................................................... 72

Appendix A. Sampled Parameters and Sampling Frequencies................................................................A-1

Appendix B. Fixed-site Sampling Locations...........................................................................................B-1

Appendix C. Instrument Performance Quality Factor Codes..................................................................C-1

Appendix D. Field Instrument Maintenance and Calibration..................................................................D-1

Appendix E. Equipment List for Water Quality Monitoring ................................................................... E-1

Appendix F. Previous Methods and Equipment....................................................................................... F-1

Appendix G. Sonde Holder for Use in Subfreezing Temperatures..........................................................G-1

Appendix H. Key to Subsurface Sampling Requirements for Off-Channel Areas..................................H-1

Appendix I. Program Code to Randomize Chlorophyll-a Sampling Sites............................................... I-1

Appendix J. Water Quality Forms.............................................................................................................J-1

 Page
x

Tables

Number Page

1. Calendar used for stratified random sampling (SRS) in the Long Term Resource

 Monitoring Program ............................................................................................................................. 3

2. Relation of Long Term Resource Monitoring Program aquatic area codes and sampling stratum

used in stratified random sampling for water quality monitoring.......................................................... 8

3. Water quality sampling strata and sampling allocations in the six Long Term Resource

 Monitoring Program study areas......................................................................................................... 13

4. Description of six quality assurance and quality control (QA/QC) sample types used in

 Long Term Resource Monitoring Program water quality monitoring ................................................ 15

5. Beaufort wind/sea-state scale.............................................................................................................. 20

6. Flow velocity classes used in the Long Term Resource Monitoring Program ................................... 22

7. Substrate particle categories based on Wentworth’s classification ..................................................... 25

8. Predominant substrate categories used in the Long Term Resource Monitoring Program................. 26

9. Recommended dilution volumes for turbidity samples greater than 100 nephelometric turbidity

 unit (NTU) .......................................................................................................................................... 35

10. Acid additions required to reach the desired pH for preservation of 60-mL Long Term

 Resource Monitoring Program water quality samples........................................................................ 54

11. Preservatives, containers, and holding times used for water quality monitoring samples in the

 Long Term Resource Monitoring Program........................................................................................ 56

12. Description of the Long Term Resource Monitoring Program (LTRMP) electronic water quality

 data sheet fields with instructions for use and reference to procedures that relate to the specific

 datasheet entry .................................................................................................................................... 63

13. Description of water quality data sheet quality factor codes used in the Long Term Resource 

Monitoring Program............................................................................................................................. 68

Figures

1. Long Term Resource Monitoring Program field stations ...................................................................... 1

2. Diagram of various depth (Z) definitions associated with ice cover and under-ice sampling ............. 23

3. Treatments used to prepare samples for shipment to the Long Term Resource Monitoring Program 

analytical laboratory............................................................................................................................. 52

4. Electronic water quality data sheet used by the Long Term Resource Monitoring Program ............ 61
water quality monitoring activities follow the 

guidelines in Standard Methods (APHA 1992). 

Likewise, the LTRMP follows the manufacturer’s 

published instructions for the operation and 

maintenance of monitoring instruments and 

equipment unless indicated otherwise by specific 

guidance in this document.

 The LTRMP trend monitoring network for 

water quality has a mixed-model sampling design 

(see Section 1.1 for additional discussion). In this 

design, a relatively small number of fixed sites are 

monitored every 14 to 28 days, and a larger number 

1. Rationale and Strategy

for Monitoring Water Quality

 The Long Term Resource Monitoring Program 

(LTRMP) monitors only selected aspects of 

water quality in the Upper Mississippi River 

System (UMRS). Study areas in the UMRS 

on the Mississippi River main stem are Lake 

Pepin and Navigation Pool 4 near Lake City, 

Minnesota; Navigation Pool 8 near Onalaska, 

Wisconsin; Navigation Pool 9, near Lansing, 

Iowa; Navigation Pool 13, near Bellevue, Iowa; 

Navigation Pool 26 near Alton, Illinois; and the 

Open River reach (sometimes called 

the Middle Mississippi River) near 

Cape Girardeau, Missouri. Sampling 

of the UMRS on the Illinois River is 

conducted on the La Grange Pool near 

Havana, Illinois (Figure 1). 

Water quality monitoring in the 

LTRMP emphasizes basic limnological 

characteristics that pertain to the 

suitability of habitat for aquatic 

organisms and the movement of 

sediment and materials within the 

system (cf. Hynes 1970). Because of 

logistic limitations, monitoring in the 

LTRMP includes only a small subset 

of important limnological variables; 

parameters of importance primarily 

for human consumptive uses are not 

measured. Standard methods are 

used in all data collection efforts 

and because the Program strives to 

document long-term trends, long-term 

consistency is maintained to the extent 

possible.

 General techniques and procedures 

for routine water quality monitoring 

and analysis are well established 

and published elsewhere (USEPA 

1974; Lind 1979; Wetzel and Likens 

1991; APHA 1992; U.S. Geological 

Survey 1999). The LTRMP uses these 

published procedures where applicable, 

and unless specific guidance in this 

document indicates otherwise, LTRMP 

Figure 1. Long Term Resource Monitoring Program field stations. Each field station 

team conducts water quality monitoring in nearby reaches of the Mississippi or 

Illinois Rivers and major tributaries.
2 

of randomly selected locations are sampled at 

seasonal intervals (quarterly).

 Before 1993, all water quality monitoring 

was done at regular intervals at fixed sampling 

locations. In this pre-1993 design, statistical 

inferences were possible only for the specific 

locations selected for sampling. Replication of 

site types (habitat classes) was inadequate, there 

was no statistical capability to extrapolate to 

larger areas or to area types, and points of unique 

or special significance (i.e., tributary inflows) 

were not adequately represented. Consequently, 

the LTRMP scientific staff revised the design in 

1992–93. This new design combined fixed-site 

sampling (FSS) with stratified random sampling 

(SRS) to allow valid statistical inferences about 

sampled strata and across entire pools over time 

while also tracking locations of special interest, 

such as tributary inflows and unique habitats. 

Further details of this design, implemented in 

1993, are in Sections 1.1.1 and 1.1.2.

1.1 General Sampling Approach 

 Water quality monitoring is conducted by the 

staffs of six field stations that collect samples 

and information from the Mississippi River and 

Illinois River main stem and adjoining tributaries. 

Each field station conducts monitoring operations 

on reaches within an 80 km (50 mile) radius of 

their base station and field teams are familiar 

with the sampled areas. The reaches covered 

by each field station are as follows from north 

to south: Lake City (field station 1, Lake City, 

Minnesota), Pools 4 and 5, including Lake Pepin; 

Onalaska (field station 2, Onalaska, Wisconsin), 

Pools 7 through 9; Bellevue (field station 3, 

Bellevue, Iowa), Pools 12 through 14; Great 

Rivers (field station 4, Brighton, Illinois), Pool 

26, Illinois River mouth, Missouri River mouth, 

and immediately below the Mississippi–Missouri 

confluence; Havana (field station 6, Havana, 

Illinois), La Grange Pool of the Illinois River; 

Open River (field station 5, Jackson Missouri), 

from the Ohio River to about 100 mi upstream of 

the confluence.

 The timing and location of water quality 

monitoring is guided by the spatial and temporal 

patterns of variance in the parameters being 

measured and by the information desired. 

The limited resources of the LTRMP and the 

large spatial expanse of the study area prohibit 

routine measurements at high frequencies (i.e., 

daily or hourly) or close spatial intervals (i.e., 

<50 m between sampling points). However, 

measurements must be at intervals of time and 

space that allow the detection of large-scale 

habitat changes and biotic responses among 

adjacent years and over long periods (i.e., 5 to 

10 years). Consequently, the routine monitoring 

is designed to detect patterns at spatial scales on 

the order of kilometers and temporal scales of 

months or seasons.

 Because the LTRMP is attempting to detect 

resource differences and similarities among the 

study reaches, as well as changes over time, the 

sampling regime in all reaches must be consistent 

and adhere closely to established protocols. 

Without this consistency, apparent differences in 

physical and chemical characteristics can result 

from differences in methodology rather than 

actual temporal or geographic variation.

 Routine water quality monitoring in the 

LTRMP is performed in two phases, FSS and 

SRS.

1.1.1 Fixed-Site Sampling Design

 The FSS is conducted by field teams at 

approximately constant intervals (e.g., 2 or 

4 weeks) at permanently designated locations. If 

the point of sampling for an FSS location is to be 

moved significantly, then a new site designator 

must be registered in the LTRMP database, and 

this is only done with the approval of the LTRMP 

water quality coordinator. In selected locations 

where distinct and persistent cross-channel 

gradients in water quality have been documented, 

multiple (3–4) fixed-sampling sites are arrayed as 

a linear transect across the channel. Compositing 

has not been used to date to reduce sample load 

as the additional complications in the field and in 

data management, combined with the reduction 

in information seem to outweigh the costs of 

analyzing these few additional samples for the 

LTRMP parameters.

 The purpose of FSS is to track conditions 

at specific locations over time (seasonal time 
3

scale and longer). Because the fixed sites were 

subjectively chosen (often to monitor unique 

conditions), they cannot be assumed to represent 

other locations of the same general type.

1.1.2 Stratified Random Sampling Design

 The SRS is used in the LTRMP for fish, water 

quality, invertebrate, and vegetation monitoring 

in the six LTRMP study reaches. This approach 

is designed to give unbiased estimates that 

can be extrapolated to entire strata, pools, and 

reaches and for making comparisons among 

strata, among pools, and over time. Random 

selection of sites eliminates many sources of 

sampling bias and produces results that can be 

extrapolated with known confidence. The use of 

defined strata allows the sampling effort to be 

adjusted to variability or ecological importance 

of targeted areas. The SRS tracks conditions at 

spatial scales corresponding to sampling strata 

or larger (i.e., whole pool or sampling reach) and 

seasonal-annual time scales or longer. Quarterly 

SRS episodes are intended to encompass major 

seasonal events (Table 1), but their scheduling 

is not changed from year to year. The allocation 

of sampling locations among the strata is 

not proportional to stratum surface area, so a 

weighting method (e.g., area based) must be 

used to extrapolate SRS means to an entire study 

reach.

 The sample collection methods used in 

SRS are identical to FSS. However, there 

are important design differences: (a) the 

sampling locations are selected with statistical 

randomization to represent specific strata 

(aquatic area types; Wilcox 1993); (b) the 

suitability of the site and its precise location 

must be determined in the field at the time of 

sampling; (c) a specific location is unlikely 

to be sampled repeatedly over time except in 

reaches where certain strata are rare; (d) SRS 

is conducted quarterly; in late January to early 

February, in late April to early May, in late July 

to early August, and in early to mid-October; 

and (e) the full suite of chemical analyses are not 

performed at SRS sites. An important concept 

of the SRS design in LTRMP water quality is 

that the measurement at an individual sampling 

location is considered a random observation 

from a population (stratum of sampling points) 

during a sampling episode (about 10 days). When 

pooled together, this set of random measurements 

provides an accurate estimate of conditions 

within the entire stratum, even though an 

individual site measurement may not be a good 

representation of typical (i.e., average) conditions 

at the specific point of sampling or across the 

whole stratum during the episode.

Table 1. Calendar used for stratified random sampling (SRS) in the Long Term Resource Monitoring Program. The primary sampling period 

begins on a Monday and extends over the next 14 days exclusive of weekends. A third week may be used if necessitated by urgent 

circumstances, safety considerations, or equipment failure. The SRS sampling schedule takes second priority if it conflicts with fixed-site 

sampling.

Sampling

period Start date Rationale

Spring Monday of last full work week in 

April

Period of maximum discharge in the Upper Mississippi River

Summer Monday of last full work week in 

July

Late summer conditions, typically low-flow period of maximal 

water temperature, minimal oxygen

Fall Monday of second full work week 

in October

Low-flow period after aquatic vegetation die-back and before 

ice formation. Period of maximum waterfowl migration. 

Moved forward a week in 1996 and 1997 to avoid conflict with 

waterfowl hunters.

Winter Monday of last full work week in 

January

Period of maximal ice and snow cover, lowest water 

temperatures, and minimal oxygen concentration.
4 

1.1.2.1 Definition of Sampling Strata

 The primary function of the sampling strata is 

statistical, and they are based on the aquatic areas 

of Wilcox (1993) as implemented by Owens and 

Ruhser (1996). Although the LTRMP sampling 

strata reflect differing habitat types, they are not 

habitat classes, and a precise correspondence 

between strata and habitat is not intended. The 

statistical validity and utility of the strata does 

not require a perfect match between mapped 

strata and habitat or aquatic areas. However, it is 

essential that the strata be defined and mapped 

quantitatively. In the LTRMP, this means the 

sampling strata are defined in a geographic 

information system (GIS).

 The LTRMP sampling strata are areas on a 

map defined by major, enduring geomorphic and 

physical features as described by Wilcox (1993) 

and quantified from 1989 aerial photography 

using a GIS. Some minor modifications were 

made using bathymetric and land cover data, as 

suggested by Wilcox (1993). Additional changes 

were requested by field personnel on the basis 

of field observations during the first 2 years of 

stratified random sampling.

1.1.2.2 Changes in Stratum Boundaries 

 To facilitate analysis of the LTRMP data, the 

boundaries of the sampling strata are intended 

to be relatively static over several years. These 

boundaries are clearly defined and reproducible 

within a GIS framework. Field teams can report 

apparent changes in strata boundaries, but 

redefining the sampling strata requires more 

extensive information. Subjective interpretations, 

or reinterpretations, of strata boundaries (i.e., by 

field teams) are not consistent or reproducible 

over time, and inconsistent changes in the 

strata boundaries would make long-term data 

interpretation difficult or impossible. Subjective 

interpretations differ among individuals, and 

modifications based on transient properties (e.g., 

river stage or flow velocities) are not appropriate. 

The collection of ancillary data during sampling, 

combined with appropriate sample comments, 

is extremely important to detect and interpret 

unusual or “nonrepresentative” conditions within 

a stratum and can provide the basis for initiating 

a quantitative remapping of the strata boundaries.

1.1.2.3 Atypical Conditions within Strata 

 Sampling strata are not expected to be 

uniform, and each individual site is not expected 

to be typical of the average physical, chemical, 

or biological conditions within the stratum. Each 

stratum is expected to contain a broad mosaic 

of habitat types, with the distribution of habitats 

differing among the strata. Unlike habitats, 

strata do not have a set of physical, chemical, or 

biotic attributes (i.e., depth, velocity, substrate 

type, vegetation) that uniquely define them. 

Habitat conditions and classifications can change 

on a scale of minutes to hours in response to 

discharge. In contrast, changes in the mapping 

of LTRMP sampling strata are done to reflect 

relatively permanent changes in the river and 

floodplain geometry. 

1.1.2.4 Changes in the River Over Time 

 Two fundamentally different approaches 

can be taken to assess spatial changes within a 

stratified sampling framework. One method is to 

frequently remap the strata on the basis of field 

observations and then attempt to track or quantify 

the mapped changes. This approach is impractical 

because of the enormous difficulties inherent 

in remapping at frequent intervals in a defined, 

quantitative, and consistent manner. Further, the 

routine field sampling in the LTRMP does not 

provide the level of spatial information needed to 

perform this remapping, so a separate, intensive 

effort would be required to support this approach. 

An alternative is to have the sampling strata 

permanently fixed in space, and then quantify 

changes in conditions within the permanently 

fixed strata based on the sampling data. This 

approach is workable and consistent with the 

LTRMP design, but over time the correspondence 

between strata and aquatic areas slowly degrades 

so that conditions within aquatic areas are not 

well tracked, even though information at the 

pool and reach scale is maintained. The LTRMP 

has implemented a compromise approach. 

Strata are relatively permanent, intended to be 
5

revised only at infrequent intervals (i.e., 5 to 10 

years) in response to major changes in system 

morphometry. Changes in conditions within the 

strata (and at the pool or reach level), rather than 

changes in the strata boundaries, are used to 

indicate short-term changes in the system.

1.1.2.5 Remapping of Sampling Strata 

 Remapping of strata requires detailed, 

objective information in the form of GIS 

coverages and cannot be based on a few 

observations. Therefore, only large, extreme 

errors have been corrected in the strata maps on 

an ad hoc basis. Smaller errors are few (typically 

less than 5% of total sites sampled) and are not 

generally corrected as they are encountered over 

short periods. However, consistent mapping 

errors are scheduled to be addressed in a major 

remap (originally planned for the year 2000). 

Data from routine SRS sampling is not adequate 

to remap the strata in the short term, but SRS 

data should be used to help guide the major 

remapping effort when eventually performed.

1.1.2.6 Spatial-Temporal Scales 

and Cross-Component Consistency 

 The explicit focus of SRS within the LTRMP 

is the pool or reach and annual scale, and the 

sampling strata are statistical tools that allow 

valid, unbiased estimates at this scale of time and 

space. Secondarily, the strata allow inferences 

about the strata themselves and, to a lesser 

degree, about habitats or aquatic areas. Patterns at 

the subannual scale can sometimes be addressed 

with the SRS data, and interpretation of SRS 

data in terms of specific habitats are sometimes 

possible. However, this must be done with care 

because the strata are geographic areas on a 

map, not habitats. To understand the ecological 

significance of patterns within strata and 

differences among the strata usually requires the 

use of ancillary information (e.g., water depth, 

sampling location, current velocity, number of 

sites, etc.). 

 Because the primary target of SRS is the 

pool (or reach) and annual scale, this is also the 

intended scale for cross-component synthesis 

or integration using the SRS data. For example, 

the water quality data from SRS is not intended 

to explain why a certain netting effort produced 

a certain result (ancillary data collected while 

netting might serve this purpose), but rather why 

catches or year classes of some species may be 

declining in a pool over several years. The strata 

used for each component need not be identical 

across components because the design is not 

intended for cross-component inferences at 

the stratum scale. Further, to make valid crosscomponent inferences at the pool and annual 

scale, the strata must differ among components. 

If, for example, the water quality sampling was 

limited to the times and locations (e.g., strata) 

used for fish sampling, conditions at times and 

places unsuited to fishing (e.g., ice cover in 

shallow backwaters), but critical to fish success 

or failure, would not be sampled. The same holds 

for vegetation and invertebrates.

 Cross-component analysis or synthesis at time 

scales shorter than years and space scales less 

than a whole pool are not prohibited by the SRS 

design, but it requires a customized approach 

to the data, and some analyses at the stratum or 

substratum level may not be fully supported. 

Appropriate ancillary information must be 

collected if small-scale, short-term processes are 

of interest and, in the LTRMP design, this finer 

scale of time and space is considered the realm of 

focused, specialized studies, rather than routine, 

long-term monitoring.

1.1.3 Other Sampling Approaches

 In addition to routine monitoring, focused 

water quality investigations within the LTRMP 

have used continuous monitoring devices (e.g., 

at 15-min intervals) placed in situ to document 

the time course of significant phenomena (e.g., 

diurnal or seasonal anoxia in specific areas). 

However, these studies are not part of routine 

monitoring, and the protocols used are not listed 

in this manual. Likewise, Lagrangian methods 

(i.e., sampling from a mass of water as it moves 

downstream) are not part of routine water quality 

monitoring by the LTRMP and are not described 

here.
6 

1.2 Sampling Schedule 

 Field team leaders are ultimately responsible 

for maintaining sampling schedules and have the 

authority to postpone sampling during unsafe 

weather periods. However, sampling is never 

rescheduled simply to take advantage of good 

weather or to avoid unpleasant conditions as 

this introduces statistical bias and can invalidate 

LTRMP results.

 To the extent possible, a single sampling 

schedule is used for water quality monitoring 

by all the LTRMP field stations. This schedule 

has undergone modifications with a major 

redesign of the Program in 1993 (Section 1, 

introduction) and less dramatic changes in other 

years (Appendix A). The daily sampling schedule 

used for water quality monitoring in the LTRMP 

is described in Section 1.3; the calendar used for 

SRS sampling is described in Table 1. Note that 

the SRS calendar takes second priority behind the 

FSS schedule. In many instances, both SRS and 

FSS can be conducted simultaneously.

1.3 Standardization and Randomization 

of Sampling Time

 Without randomization of the sampling 

route and consistency among sampling teams in 

scheduling of the workday, the short-term effects 

of time (i.e., daily cycles) are confounded with 

the effects of stratum or sampling location. 

 In SRS, the differing strata should be sampled 

evenly across an entire sampling episode. For 

example, all the “side channels” cannot be 

sampled on day 1 and all the “backwaters” on 

day 2, nor can the main channel sites be sampled 

primarily in the morning and backwaters in the 

afternoon. Because of logistical constraints, one 

longitudinal section of the river may be sampled 

on one day and another the next, but to the extent 

possible, sampling of strata within the workday 

and across the entire sampling episode must be 

randomized. Sometimes, this is accomplished by 

randomly selecting a map panel (e.g., 5 to 10 km2

of study area) for each day or half-day of work 

and then sampling all sites on the panel, but in 

other situations a more sophisticated approach is 

used.

 Randomization of sampling times or site 

order must be closely observed. Sampling order 

for SRS is randomized by panels, workdays, or 

other suitable methods in advance of sampling. 

This randomized order must be adhered to and 

is not modified to adjust for field conditions. 

In FSS, the sampling route is varied randomly 

within logistic constraints so that (1) sites are 

not sampled in the same sequence during each 

sampling day and (2) differences among study 

reaches are not confounded by differences in 

work schedule. At a minimum, the sampling 

route is reversed at random (i.e., by coin toss 

before leaving the field station). This keeps 

cyclic, diel variation from contaminating the 

long-term results of SRS and FSS.

 Sampling times for FSS and SRS are 

standardized among all field stations and remain 

unchanged over the course of the year. Beginning 

in April 1994, a standard workday for sampling 

was established for SRS and FSS water quality 

monitoring. This workday is based on central 

standard time and is unaffected by changes 

in the clock because of daylight savings. The 

schedule for each workday is centered on noon, 

such that the mean of sampling times during 

a day is as close as practical to 1200 hours, 

and sampling should not be conducted before 

0800 hours or after 1600 hours. The need for 

this standardization is clearly evident in the 

LTRMP water quality data collected before 1994 

(FSS only). In these data, the effect of daylight 

savings time on the work schedule confounds 

the effects of diel variations with the effects 

of season. Likewise, before 1994, consistent 

differences in the work schedule among field 

stations confounds diel variation with geographic 

location.

1.4 Geographic Coordinates

 Geographical positions in the LTRMP are 

identified using Universal Transverse Mercator 

(UTM) grid coordinates. This rectangular 

coordinate system identifies a location by its 
7

distance (in meters) east (easting) and north 

(northing) of reference lines on a transverse 

mercator chart. The reference lines for the easting 

and northing distances are defined by the UTM 

zone.

 In LTRMP water quality monitoring, the 

geographic coordinates of all sampling locations 

are defined by reference to a base map. The 

geographic location (UTM coordinates) of 

each LTRMP water quality sampling location 

is registered in the LTRMP central database. 

These coordinates may be corrected or verified 

by additional field measurements, but the 

physical location of a sampling site does not 

change over time. Whenever a new location is 

sampled, this is registered as a new, unique site 

in the LTRMP database. A site cannot be moved. 

Changing a sampling location is accomplished 

by establishing a new site and discontinuing 

monitoring activity at the previous location. 

Various techniques are used to locate sampling 

locations in the field, including global positioning 

system (GPS) equipment and visual landmarks. 

The UTM coordinates of FSS locations are 

determined when the site is first established and 

the coordinates for SRS sampling are published 

in advance. Consequently, UTM coordinates 

are not recorded on the data sheet (Section 8.3) 

except during special project monitoring and then 

only at sites that have not been registered in the 

LTRMP database.

1.5 Fixed-site Sampling Locations 

 The LTRMP sampling of fixed sites is 

intended to provide a relatively continuous 

record of limnological conditions and constituent 

concentrations at (1) major inflow and outflow 

points of the LTRMP study reaches and 

(2) locations of special long-term interest. The 

locations selected for FSS are used only to 

represent the sampling point and, for tributaries, 

the contributions from the watershed upstream 

of the sampling site. See Appendix B for a list 

of location codes and descriptions of fixed-site 

water quality sampling locations.

1.5.1 Main Stem Location Codes

 Main stem location codes are used to 

designate routine FSS sites in the Mississippi and 

Illinois Rivers and associated backwaters. This 

system was established in 1988 at the start of the 

Program and was not changed in the redesign 

of 1993. The codes are based on the distance 

upstream (river miles) from the river mouth or 

major confluence and on the relative left to right 

(facing upstream) location of the site between the 

river bluffs. Main river site codes for FSS have 

the form:

 Axxx.xB

where

 A is a one-letter designator for the river 

(I = Illinois River; M = Mississippi River),

 xxx.x is the distance in stream miles (with 

tenths) upstream from the confluence with 

the main river (padded with leading zeros 

as needed to result in four digits), and

 B is a suffix (A–Z) that indicates the 

relative distance from the left ascending 

bluff (i.e., on the left looking upstream; 

A is the left bluff, Z is the right bluff, 

M is midway between bluffs). For 

example, site M245.1M is a site on the 

Mississippi River, at River Mile 245.1 

(245.1 mi upstream from the Ohio River 

confluence), midway between the left 

and right bluffs. This suffix assignment 

is done by reference to an appropriate 

topographic map or navigation chart, 

but is only a rough indicator of site 

location that is defined more precisely by 

geographic coordinates.

 See Appendix B for a list of main stem 

location codes.

1.5.2 Tributary Location Codes

 Tributary location codes are used to designate 

routine FSS sites only when the sampling is 

done in the tributary itself, upstream from its 

confluence with the main river. Otherwise, the 

main river nomenclature applies. Tributary 
8 

location codes for FSS are similar to main stem 

locations and have the form:

AAxx.xM

where

 AA represents a one- or two-letter 

abbreviation of the tributary name,

 xx.x is the distance in stream miles (with 

tenths) upstream from the confluence with 

the main river, and

 M is a suffix (A–Z) that indicates the 

distance from the left bank of the tributary 

looking upstream at main river sites 

(i.e., A is the left bank, Z is the right 

bank). The letter M is used to designate 

midtributary sampling. For example, 

AP01.1M indicates a midchannel site on 

the Apple River, 1.1 mi upstream from 

its mouth. As with main stem sites, the 

site coordinates define the location more 

precisely.

 The distance in stream miles is padded with 

leading zeros as needed to bring the entire 

location code to a length of seven characters 

(including the decimal point). See Appendix B 

for a list of tributary location codes.

1.6 Stratified Random Sampling Locations

 The SRS for water quality is based on six 

aquatic area strata (Wilcox 1993; Table 2). 

From 1993 through January 1995, the sampling 

strata were divided into rectangular north–south, 

east–west grids with 200 m between grid lines in 

all strata. Beginning with spring 1995 SRS, this 

was changed to 50 m between grid lines in the 

contiguous backwater and side channel strata. All 

other strata remained at 200-m grid spacing. The 

higher density grid is appropriate here because 

the data have shown greater spatial variability 

within these strata. The sampling grid is used for 

selecting sites, but the geographic coordinates 

(UTM) of each site are used to locate the site in 

the field and the site identifier (described later) 

makes no reference to this grid. 

 The number of sampling strata, total number 

of sampling sites, and the allocation of sampling 

sites among the sampling strata was based on 

several factors: (1) analysis of 1988-92 sampling 

that showed the number of sites that could be 

sampled in about 2 weeks (10 workdays) and the 

relative levels of variance to be expected in the 

differing strata, (2) consultation with the field 

Table 2. Relation of Long Term Resource Monitoring Program aquatic area codes and sampling stratum used in stratified random 

sampling for water quality monitoring. Aquatic areas are based on Wilcox (1993).

Stratum

 Aquatic

area codes Code Description

1501 1 Main channel (MC)

1504 2 Side channel (SC)

1510 3 Backwater area contiguous to the main channel at low water 

conditions (BWC)

1513 4 Lake Pepin or Swan Lake (Lake)

1520 5 Open water area above the dam influenced directly by impoundment 

(IMP)

1530 6 Isolated, no surface connection to the main channel (BWI)

N/A 7 Aquatic areas that have been dewatered for extended periods so that 

terrestrial vegetation has become established. This includes areas that 

have become terrestrial at normal water elevations.
9

teams to verify the results of the data analysis, 

(3) a desire to detect differences in single variable 

and multivariable means at about the 10% level 

among strata or sampling episodes with good 

statistical reliability (P < 0.10), and (4) extensive 

monitoring experience and professional best 

judgment. The allocation of sampling locations 

among the strata is not proportional to strata 

surface areas or volumes, so weighting is 

required to extrapolate stratum means to broader 

areas (e.g., an entire study reach).

 For each study reach (field station) and 

SRS sampling episode, three sets of sampling 

locations are drawn at random and without 

replacement from the list of available sites 

within the study reach. The sites selected within 

each of these three groups are then numbered 

consecutively within strata in north to south (top 

to bottom) columns that progress from west to 

east. The numbering sequence by strata is BWC 

(backwaters, contiguous), BWI (backwaters, 

isolated), IMP (impounded areas), Lake (Pepin 

or Swan Lake), MC (main channel), and SC 

(side channels). The first group of selected 

sites are the primary sampling locations that 

are monitored for a full suite of parameters. 

The second group is drawn randomly and 

without replacement from locations that were 

not selected in the first drawing. This second 

group of sampling locations is monitored for a 

reduced or partial suite of parameters, including 

all in situ measurements, plus chlorophyll-a

and suspended solids (see parameter list in 

Appendix A). Site numbering of this second 

series continues the numbering sequence of the 

first series and a “P” suffix (partial) is added to 

the site number. Finally, a third group of sites is 

randomly selected from those not chosen in the 

first two drawings. This third group is used as 

alternate sampling locations that substitute for 

sites in the first two series that are unusable (see 

Section 1.8 for more details on alternate site use). 

Site numbering of this third series continues the 

numbering sequence of the second series and an 

“A” suffix (alternate) is added to the site number. 

Site numbers are, therefore, a single continuous 

series, and the actual stratum associated with a 

sampling site and the UTM coordinates of the 

site are recorded as separate fields in the LTRMP 

database.

 In the initial summer and fall SRS sampling 

episodes conducted from July through September 

1993, the site numbering system differed from 

all subsequent episodes. In just these first two 

episodes, site numbering within each of the three 

site categories (primary, partial, and alternate) 

was consecutive, starting at site number 1. 

The sequence numbers in each category were 

converted to a unique value by adding an offset 

of 100 to “P” (partial parameter) sites and 

an offset of 200 to “A” (alternate) sites. This 

approach was extremely vulnerable to errors and 

was confusing for field teams. It was replaced 

by the system described above in all subsequent 

SRS sampling episodes.

 Within a sampling episode and study reach 

(field station), each SRS site identifier is unique, 

but the same site identifiers are reused in other 

episodes and in other study reaches. Additional 

identification is thus required to uniquely identify 

an SRS location in the LTRMP database; this is 

provided by the data sheet serial number (sheet 

bar code) and a permanent location code.

 Site identifiers used in the field (and on data 

sheets) for stratified random sampling have the 

form:

NNNx

where

 NNN is the sequential site number within the 

episode and

 x is a suffix that indicates site category 

as follows: no suffix = full parameter, 

primary sampling site; suffix A = alternate 

site (may be used for full or partial 

parameter); suffix P = partial parameter 

site.

 In addition to the temporary field identifier, 

each SRS location is assigned a unique sevendigit location code of the form:

YYFENNN

where

 YY is the calendar year (e.g., 01 for 2001, this 

system must be revised before 2093),

 F is the field station identifier (1 = Lake 

City, 2 = Onalaska, etc.),

 E is the seasonal episode (1 = spring, 

2 = summer, 3 = fall, 4 = winter), and
10 

 NNN is the field identifier with any suffix 

omitted.

 Stratum type and UTM coordinates 

(in meters) for each site are permanently 

registered in the LTRMP database. The strata 

codes (Table 2) are used in the registered site 

descriptions and were chosen to be consistent 

with the aquatic areas/land use spatial data 

coverages maintained in the ARC/INFO 

software environment at the Upper Midwest 

Environmental Sciences Center (UMESC).

1.7 Locating Stratified Random Sampling 

Locations in the Field

 In SRS, sites are located by reference to 

a base map. The SRS sites are not defined as 

points, but circular areas with either a 25 or 

100 m radius. The smaller radius circle is used in 

side channels and backwaters, the larger radius 

applies to all other sampling strata. The SRS 

samples are taken to represent the general habitat 

stratum, not the exact sampling point. Although 

it is critical that the sampling site be suitable 

and randomly selected, it is not necessarily at 

the exact preselected coordinates (center of the 

sampling circle), although field teams make a 

concerted effort to sample from the center point 

of the predefined sampling circle if possible and 

appropriate.

 If the center of the sampling circle (see 

previous paragraph) is unsuitable (e.g., dry land 

or other obstruction), the field team can use 

the appropriate procedure (described later) to 

select another point within the sampling circle. 

Although close positional accuracy (e.g., less 

than half the radius of the sampling circle) 

is not required, field teams exercise care and 

professional judgment to ensure that the actual 

point of measurement is randomly chosen and 

that personal bias (e.g., preference for shady 

areas, absence of aquatic vegetation, calm, or 

deeper water) does not influence the selection 

process. If a suitable sampling point cannot be 

found or accessed within this sampling circle, 

then an alternate site is used (Section 1.8.2). 

 When the central position of a predefined 

sampling location is unsuitable or inaccessible, 

but suitable sampling can be performed within 

the site radius (25 or 100 m), the field team 

uses the following procedure to select another 

location:

 a. Use the suitable location that is nearest to 

the center of the sampling circle. 

 b. If several nearby sites are suitable and 

approximately equidistant from the center, 

the more upstream of the available choices 

is used.

 c. If proximity and upstream-downstream 

priority cannot be clearly established, 

then the nearest site to the right (looking 

upstream) of the center is selected.

 A simple mnemonic (memory helping) phrase 

may be helpful; e.g., “Close Up is Right where 

you want to be.”

 Prior to the fall 1998 SRS episode, whenever 

possible, the field crews were required to sample 

within one-half of the sampling radius (i.e., 

one-half of 25 m in BWC and SC = 12.5 m, 

and one-half of 100 m in other strata = 50 m). 

When those criteria could be met, a site type of 0 

(Primary) and a Position Method of 1 (Base map) 

were assigned. In the event that close positioning 

could not be obtained, but a suitable sampling 

location existed within the sampling radius (see 

previous discussion in this section), then a Site 

Type 3 (other) was assigned, GPS coordinates 

were recorded, and the Positioning Method was 

recorded as 2 (GPS). Beginning in fall 1998, 

positioning requirements were changed to those 

discussed previously. For all practical purposes, 

positioning requirements were not affected, as 

the crews still must sample within the sampling 

radius and as close to the center of the circle as 

possible; however this did result in a change to 

the recording methods.

1.8 Use of Alternate Sites

in Stratified Random Sampling

1.8.1 Requirement to Sample an Alternate Site

 If water depth (Zmax; Section 3.1) of a 

sampling location is <0.2 m (but the site is 

inundated at normal water levels) or the site 

cannot be sampled because of intervening dry 

land or other impassible conditions, then the 

use of an alternate site is strongly encouraged 
11

due to the difficulty associated with obtaining a 

clean sample. However, alternate site sampling 

must be performed within the limits of the daily 

sampling window and if extensive areas are 

dewatered or inaccessible, then field teams must 

consider the upper limit on use of alternate sites 

(Section 1.8.3). Field teams should not exclude 

a site (and use an alternate) because the site 

does not appear representative of the designated 

stratum. If a site can be sampled, then sampling 

should be performed. Special characteristics of 

the site should be recorded as site comments and 

flagged by the use of appropriate site summary 

codes and field-derived stratum codes.

1.8.2 Picking an Alternate Site 

 If a suitable sampling location does not 

exist within the 25- or 100-m sampling radius 

appropriate to the stratum, then a site from the 

alternate site list is used. This site is chosen 

by examining the available alternate sites and 

picking the one that is closest to the rejected site 

and within the same sampling stratum. If two or 

more sites are approximately equidistant from the 

rejected site, the procedure to select one of these 

is the same as that used to select a sampling point 

within the sampling circle (“Close Up is Right

where you want to be,” Section 1.7).

 If the alternate site is distant, it should be 

sampled when it is efficient to do so (e.g., other 

sites are in the same vicinity). All sampling 

scheduled for the original site (i.e., collection 

of samples for chemical analysis) is performed 

at the alternate site. If the original site was 

designated for quality assurance and quality 

control (QA/QC) sampling, then the alternate 

site should be used in this capacity if it is 

sampled by the same field team and on the same 

day. Otherwise, another QA/QC site must be 

randomly selected from those that remain on the 

day’s sampling plan. A datasheet header for the 

original site must be filled out, bar coded, and 

appropriate site comments recorded (e.g., “site 

replaced by alternate site number 151a”).

 Sampling order for SRS is randomized by 

panels, workdays, or other suitable method in 

advance of sampling. This randomized order 

must be closely adhered to and is not modified to 

adjust for river conditions.

1.8.3 Limits on the Replacement of Primary Sites 

with Alternates 

 Alternate sampling sites for SRS have been 

used infrequently in Pools 4, 8, and 13; mostly in 

winter when ice extends to the substrate. In the 

lower reaches of the system (Pool 26, La Grange 

Pool of the Illinois River, and Open River), 

water level fluctuations are more extreme, and 

the use of alternate sites is more common. In 

these study reaches, the entire backwater or side 

channel stratum may be dewatered or rendered 

inaccessible and this requires creative approaches 

to the use of alternate sites.

 Case 1. A small portion of the stratum cannot 

be sampled. The free substitution of an alternate 

location within the sampling circle (Section 1.7) 

is often adequate for these situations. The nearest 

site on the alternate list can also be used.

 Case 2. A large portion of the stratum cannot 

be sampled. The sampling effort should be 

redistributed across the portion of the stratum 

that remains usable. This situation requires 

prior knowledge of the sampling conditions and 

the extent of suitable sites; advanced scouting 

of the stratum is probably needed. Conditions 

must remain stable for a few days if this strategy 

is to be successful. The inaccessible areas are 

determined in advance, the sampling sites 

affected are counted, and replacement sites are 

then chosen at random from the alternate list. Site 

selection can be accomplished by randomizing 

the list of alternates for the stratum, and then 

picking the sites in order until a full set of 

replacements has been chosen. Randomization 

of the alternate list is required in this situation 

because the site list is generated in a geographic 

(north-south, west-east) sequence. Alternate 

sites in the inaccessible areas are excluded from 

this reselection. If the list of alternate sites is 

exhausted before all the inaccessible sites are 

replaced, additional sites can be generated in 

consultation with the component coordinator. 

The need for advanced notice is clear, but may 

not be possible in many instances. This approach 

is not appropriate when the usable portion of 
12 

the stratum is already heavily sampled (i.e., 

sampling exceeds about 3% of the total available 

sites within side channels or backwaters or about 

15% of the total sites in the main channel). 

The sampling grid is 16 times more dense in 

off-channel areas than in the main channel, 

so a larger percentage of the total sites in the 

main channel can be sampled without reaching 

the same number of samples or percentage of 

area as in the off-channel strata. Using a rough 

estimate of the area rendered inaccessible and the 

information in Table 3, the increase in sampling 

intensity that will result from reallocation of sites 

to the remaining area can be estimated.

 To illustrate Case 2, an example from 

La Grange Pool can be used. Suppose that only 

48 of the 80 selected backwater sites (60%) in 

the study area remain usable or accessible (32 

have become inaccessible). Because the sites 

are randomly selected, this implies that only 

about 60% of the total stratum is still available. 

Table 3 indicates that there are 4,197 sites in 

the full stratum, so about 2,518 (60% of 4,197) 

should be usable. Because the upper limit on 

backwater sampling is 3% of the available sites, 

the maximum number of sites required is now 

about 76 (3% of 2,518). Because 48 original sites 

remain available, 28 alternate sites (48 + 28 = 76) 

now need to be selected. 

 Case 3. No sites are usable within the stratum 

or the usable, primary sites exceed the suggested 

sampling percentage for the area that remains. 

In this instance, no alternate sites are used. 

However, data sheets are completed for the 

missed sites to the extent appropriate and the 

comment section on each data sheet indicates that 

the site was inaccessible. Additional details are 

provided in the comments as appropriate.

1.9 Site Location Maps

 For SRS, each field station is provided with 

electronic files (ASCII text format) that list the 

site identifiers, geographic coordinates, and 

stratum codes for primary, partial, and alternate 

sites. In these files, partial parameter sites 

(in situ, plus fluorometric chlorophyll-a and 

suspended solids; Appendix A) are listed with a 

“P” suffix; alternate sites are listed with an “A” 

suffix. For each field station, there are 120 to 150 

sites. Of these, 35 to 80 are full-parameter sites, 

and the remainder are partial parameter sites 

(Appendix A). Approximately 150 alternate sites 

are also provided. The field teams use suitable 

GIS software (e.g., ArcViewtm) to plot these 

sampling locations on a map of the sampling 

area.

2. Quality Assurance and Quality Control 

(QA/QC)

 The LTRMP QA/QC procedures are designed 

to quantify the reliability of the water quality 

data and allow identification of specific sources 

of error or variance. Various recommendations 

or requirements for QA/QC have been published, 

especially with regard to sample frequency, 

and these should be consulted for additional 

background and specific details (USEPA 1974; 

APHA 1992, 1998). The approach to QA/QC 

used in LTRMP water quality monitoring 

corresponds generally to the recommendations 

of Standard Methods (APHA 1998) with minor 

modifications.

2.1 QA/QC Samples for Chemical Constituents

 Standard Methods (APHA 1992, 1998) 

recommends that a minimum of 5% of each type 

of chemical measurement should be accompanied 

by QA/QC measurements. In LTRMP water 

quality monitoring, each field team attempts 

to perform QA/QC measurements at about 

5% (1 in 20) of all sites sampled during each 

sampling day. To gage team performance in the 

LTRMP water quality component, each separate 

sampling team or laboratory team performs at 

least one full QA/QC series during each day of 

operation or field sampling. Because a field team 

rarely samples more than 20 sites in a single 

day, the daily team requirement exceeds the 5% 

recommendation in almost every instance and 

results in QA/QC measures being performed at 

about 15% of all sites. In the event that a field 

team visits more than 29 sites in a single day, 

a second QA/QC sample is required to comply 
13

Table 3. Water quality sampling strata and sampling allocations in the six Long Term Resource Monitoring Program (LTRMP) study areas.

Study 

areas

Sampling 

stratum

Fraction of study 

area within the 

stratum

 (%)

Number of 

potential sampling 

sites in the 

stratuma

Number 

of sites 

assigned

Fraction of 

sites sampled

 (%)

Fraction of 

total effort

(%)

Lake 

City 

(Pool 4)

Main channel 8 310 25 8.1 19

Side channel 5 2,887 30 1.0 22

Backwater 16 9,203 50 0.5 37

Lake Pepin 66 2,441 30 1.2 22

Impounded 0 B B 0.0 0

Isolated 4 165 B 0.0 0

Totalb 99 15,006 135 0.9 100

Onalaska 

(Pool 8)

Main channel 14 314 25 8.0 17

Side channel 16 5,522 30 0.5 20

Backwater 20 7,067 60 0.8 40

Impounded 40 869 25 2.9 17

Isolated 1 31 10 32.3 7

Totalb 92 13,803 150 1.1 100

Bellevue 

(Pool 13)

Main channel 24 675 30 4.4 20

Side channel 7 3,219 30 0.9 20

Backwater 25 11,242 60 0.5 40

Impounded 32 890 30 3.4 20

Isolated 1 29 0 0.0 0

Totalb 89 16,055 150 9.3 100

Brighton 

(Pool 26)

Main channel 52 1,215 20 1.6 17

Side channel 16 5,983 42 0.7 35

Backwater 4 1,658 29 1.7 24

Swan Lake 0 237 15 6.3 12

Impounded 2 44 15 34.1 12

Isolated 6 145 0 0.0 0

Totalb 81 9,282 121 1.3 100
14 

with the 5% requirement (i.e., 5% of 30–49 sites 

rounds to 2). There is no carryover of QA/QC 

from day to day. For example, if a field team 

performs two QA/QC samplings in one day, this 

does not eliminate the requirement for a QA/QC 

site on the following day. Likewise, the number 

of sites sampled on one day does not influence 

the number of QA/QC sites required for the same 

field team on the following day (at least one QA/

QC site is required).

2.1.1 QA/QC Sampling Types

 

 In LTRMP water quality monitoring, six 

types of QA/QC samples are defined for field 

use (Table 4). These sample types are intended 

to evaluate the effects of natural variability 

and sample collection and processing on field 

measurement precision (repeatability) and 

accuracy. These checks are separate, but similar 

to, QA/QC measures performed daily in the 

LTRMP water quality laboratory to evaluate 

analytical performance. As of the date of 

publication, LTRMP water quality monitoring 

did not use field additions of known constituents 

(spikes) to evaluate accuracy. 

2.1.2 Selection of Sampling Sites for QA/

QC Measurements 

 Because SRS and FSS are considered separate 

efforts with differing site types and collection 

requirements, the 5% QA/QC requirements for 

these two portions of the sampling design are met 

separately. However, the daily QA/QC check on 

each deployed sampling team can be performed 

in association with either SRS or FSS sampling.

 For SRS, the team or crew leader uses past 

experience and best professional judgment to 

estimate how many days it will take to complete 

the SRS episode. The team or crew leader then 

calculates how many sites will have QA/QC 

measurements added to obtain QA/QC sampling 

at 5% of the total sites in the episode. Rarely, 

sites in excess of the one/crew/day requirement 

must have QA/QC measures added to meet the 

overall 5% requirement; this can only occur 

when an SRS event is completed rapidly (less 

than 4–7 days, dependent on the number of 

sites allocated to the study reach). If additional 

sites must have QA/QC performed, then they 

should be randomly selected from the entire 

Table 3. Continued.

Study 

areas

Sampling 

stratum

Fraction of study 

area within the 

stratum

 (%)

Number of 

potential sampling 

sites in the 

stratuma

Number 

of sites 

assigned

Fraction of 

sites sampled

 (%)

Fraction of 

total effort

(%)

Jackson 

(Open 

River)

Main channel 90 1,298 75 2.7 50

Side channel 7 1,689 75 3.8 50

Totalb 98 2,987 150 3.3 100

Havana 

(La 

Grange 

Pool)

Main channel 22 623 35 5.6 26

Side channel 1 558 20 3.6 15

Backwater 9 4,197 80 1.9 59

Impounded 0 0 0 0.0 0

Isolated 0 0 0 0.0 0

Totalb 32 5,378 135 2.5 100

a

Total potential sites reflect a 200-m grid in most strata but a 50-m grid in side channels and backwaters.
15

group of SRS sites before the episode begins. 

However, to greatly increase efficiency, QA/QC 

sites should also correspond to a chlorophyllcalibration/phytoplankton-collection site. The 

spectrophotometric chlorophyll (CHLS) samples 

are collected for fluorometric chlorophyll 

(CHLF) calibration at approximately 10% of the 

CHLF sampling sites (phytoplankton samples are 

also collected at these locations). Because more 

CHLS sites than QA/QC sites are required (10% 

vs. 5%), a subset of the CHLS sites should be 

used for QA/QC. Specific guidelines for selecting 

these two types of sites together are provided in 

Section 7.7.

 In FSS, as in SRS, each field team randomly 

selects a daily QA/QC site from the day’s 

schedule of sites. This single site will exceed 

the 5% requirement unless more than 29 fixed 

sites are sampled in a single day (this has never 

occurred in LTRMP and is almost impossible 

under the present design).

 When one field team participates in both 

FSS and SRS on a single day, the procedure for 

QA/QC site selection is modified slightly. The 

daily team QA/QC check may be done with the 

QA/QC site selected for FSS (because the FSS 

site will include all routine sampling parameters). 

However, QA/QC measurements are still required 

at those SRS sites (if any) that were originally 

designated as additional QA/QC sites in excess 

of the daily crew requirement needed to meet the 

5% requirement for the SRS episode. If multiple 

teams are in the field, it does not matter which 

team performs QA/QC checks at these additional 

SRS sites, as long as each field team performs its 

daily QA/QC check.

 The advantage of performing both SRS and 

FSS sampling on the same day with a single team 

is that an additional field team (with its own daily 

QA/QC requirement) need not be deployed to 

sample a small number of fixed sites (e.g., less 

than five). The one site used for the daily team 

Table 4. Description of six quality assurance and quality control (QA/QC) sample types used in Long Term Resource Monitoring 

Program water quality monitoring.

Sample type Description

Routine A sample or measurement collected in the usual way at the sampling site. This is not a separate QA/

QC sample, but is included here because a routine sample is required along with the following sample 

types to complete the QA/QC evaluation at a site.

Split A sample that is as identical as possible to the routine sample. This sample is used to evaluate 

laboratory precision and the variability introduced by field handling or processing. To obtain a suitable 

split, the routine and split samples are both taken from a single, fully mixed container of processed 

(e.g., filtered) water.

Split plus 

spike

A split sample to which a precisely defined quantity of analyte has been added. This sample is used 

to determine laboratory accuracy, practical detection limits, and to detect problems in analytical 

technique, field handling, or preservation of samples. The routine sample, split, and split plus spike 

are all taken from a single, mixed container of processed (e.g., filtered) water.

Blank A sample processed in the same manner as a routine sample, but with reagent grade water 

(Section 7.11) used instead of ambient water as the initial sample. The blank is used to check for 

contamination in the analytical water supply or sample containers, or contamination and losses during 

handling and storage. It is also used to evaluate accuracy and precision near the detection limits of the 

laboratory. Water used for blanks must be reagent grade or better (Section 7.11).

Blank plus 

spike

A blank sample to which a precisely defined quantity of analyte has been added. A blank plus spike 

sample tests for laboratory accuracy in the absence of any interfering materials or organisms. It gives 

a second verification of the spike quantity and the background Ablank@ value of laboratory grade water. 

It also provides verification of the effects of sample handling and storage.

Replicate A second, separately collected sample taken in the same manner as the routine sample but separated 

by a short interval (2B5 min). This sample provides information on the natural random background 

variability in the system.
16 

QA/QC check cannot satisfy the 5% overall 

requirement for both the SRS and FSS, but 

normal operations (less than 29 sites per day per 

team) will still exceed the 5% requirement, and 

this approach can thus save significant time and 

reduce analytical sample load.

2.1.3 Incomplete QA/QC

 When a QA/QC site is inaccessible in SRS, 

routine procedures are used for site replacement 

(Section 1.8). When a site scheduled for QA/

QC under FSS cannot be sampled, QA/QC is 

performed at a site picked at random from those 

remaining on the daily schedule. In the event 

that no additional sites are scheduled for that 

day or continued sampling is not possible, then 

one acceptable approach is to designate the final 

sampling site of the day as the QA/QC site. 

However, samples for this alternate site may be 

available only if water is being returned to the 

field station for processing, and no immediate 

action in the field is required in this instance. 

When QA/QC sites are missed because of 

inaccessibility or transportation problems, the 

team leader should ensure that the overall 5% 

QA/QC requirement is still met for the sampling 

episode (SRS) or the week (FSS).

 If the QA/QC site may be reached and is 

suitable for sampling, but other equipment failure 

prevents completion of the full suite of QA/QC 

measurements, then a partial completion of the 

QA/QC is acceptable, but must be explained in 

the site comments. In the event of equipment 

failure or other event that halts sampling for the 

day, the field team leader must, to the extent 

possible, ensure that all requirements for sample 

holding and storage are met and that deviations 

are documented in the site and sample comments.

2.1.4 Collection and Processing of QA/QC 

Samples and Measurements 

 On each field sampling day, each field team 

collects QA/QC samples and measurements 

at each site designated for QA/QC 

(Section 2.1.2). The following measures and 

parameter groups are included in field QA/QC 

measurements: water temperature, dissolved 

oxygen, pH, specific conductivity, turbidity, 

dissolved inorganic nitrogen (DIN), dissolved 

metal ions (MET bottle), soluble reactive 

phosphorus and chloride (SRP bottle), suspended 

solids, spectrophotometric chlorophyll-a (CHLS 

planchet), fluorometric chlorophyll-a (CHLF 

tube), and total nitrogen and phosphorus (TNP 

bottle). Because they are inherently imprecise 

or difficult to control or replicate, the following 

measurements are excluded from QA/QC: 

current velocity, current direction, maximum 

water depth, phytoplankton, Secchi disk 

transparency, substrate, vegetation, wave height, 

and all measurements of snow and ice cover. All 

QA/QC samples are collected and processed in 

a manner compatible with the descriptions in 

Table 4. Except for travel, a QA/QC site requires 

the sample collection and processing time of 

approximately five routine sites.

 Samples for QA/QC (Table 4) are collected 

and handled exactly as routine samples 

(Section 7) with the following modifications and 

special considerations:

 a. Split sample. A split sample must resemble 

the original, routine sample as closely as 

possible and is part of the routine sample 

until it is finally poured into its own 

sample bottle for shipment or addition of 

spike. All filtration and preservation (e.g., 

addition of acid) is performed before the 

split is separated from the routine sample. 

Because the original sample volume 

required to prepare the routine, split, and 

spiked samples may sometimes exceed 

the volume of a single grab, the necessary 

volume can be obtained by combining 

(compositing) multiple grab samples into 

a single container before proceeding with 

sample processing (e.g., filtering and 

preservation). For samples that are filtered, 

filtration is done into a single, common 

pool of filtrate, also derived from the 

single, original sample. The routine and 

split containers are filled from this single 

pool of filtrate only after the total volume 

of filtrate required to fill all necessary 

containers has been generated. When 

parameters with differing preservation 

requirements are taken from the common 
17

pool of filtrate, the parameters requiring 

addition of a common preservative (e.g., 

nitric acid) are separated into a subpool 

and preserved before further splitting into 

individual sample containers. The original 

sample must be kept well agitated during 

subsampling and filtration.

 Routine and split samples for sensor 

readings (temperature, dissolved oxygen, 

pH, and conductivity) are obtained 

from two sequential measurements 

from the sonde, separated by the usual 

3–5-sec interval between readings after 

the instrument has stabilized. These 

readings are taken in situ and are not 

“split samples” in the strictest sense, as 

differences in the readings may reflect 

either ambient changes or instrument 

fluctuations. However, they do give an 

indication of the fundamental variability in 

the readings.

 b. Spiked sample. Spiked samples are 

obtained by adding a precise defined 

volume of known composition (spike) 

to split samples (either routine or blank 

splits). The addition of spike is done at the 

same time as the original and split samples 

are processed (e.g., placed into their final 

shipping container). Spikes (1.00 mL) 

are provided to the field teams by the 

analytical laboratory in labeled, 50-mL 

volumetric flasks (polycarbonate, same as 

sample bottle). The analytical laboratory 

provides spikes for four chemical sample 

types (DIN, MET, SRP, and TNP). Spikes 

for suspended solids, chlorophyll-a, and 

phytoplankton are not used. The field 

team generates the spiked sample by 

adding completely processed sample water 

(filtered and preserved as appropriate) to 

the volumetric flask, making up a total 

volume of exactly 50.0 mL (bottom of 

meniscus). The sealed volumetric flask is 

then labeled, logged, and shipped to the 

analytical laboratory in the same manner 

as all other samples (Section 7). Sample 

depth and sonde readings are not recorded 

for spiked samples.

 c. Blank sample. The blank sample for 

QA/QC is processed exactly as any other 

sample (including filtration, acidification, 

and splitting), except that analytical 

grade water (Section 7.11) is used as the 

sample source. Sample depth and sonde 

measurements are not recorded for sample 

blanks, but a turbidity measurement is 

required. Note that the analytical water 

taken into the field for preparation of 

blanks must be kept tightly sealed when 

not in use and care must be taken to ensure 

that contaminants are not introduced 

into the container while it is opened. 

The analytical water should be discarded 

at the first sign of contamination, or if 

contamination is suspected, or at the end 

of the sampling day.

 d. Replicate sample. Replicate samples are 

obtained from a completely independent 

grab and a separate set of sonde 

measurements, usually taken 2–5 min 

after the routine grab sample. Readings for 

temperature, dissolved oxygen, pH, and 

conductivity should be taken as closely as 

possible to the same time as the replicate 

grab sample.

2.2 Equipment Calibration

 The performance of all measuring equipment 

must be verified at regular intervals to ensure 

accurate (i.e., unbiased and precise) results. 

In LTRMP water quality monitoring, most 

monitoring instruments are calibrated at the start 

and end of each sampling day and whenever 

unusual or questionable behavior is noted. 

For some sensors (e.g., temperature), less 

frequent calibration is required unless operation 

appears abnormal. The results of calibrations 

are recorded and control charts are maintained 

on all instruments. The serial number of the 

multiparameter instrument used to collect 

field readings is recorded on the data sheet. 

To document the performance of individual 

instruments or sensors during the sampling 

day, quality factor (QF) codes are assigned to 

each instrument reading (Sections 2.3 and 8.4). 
18 

Guidelines for assigning these codes are in 

Appendix C. 

2.3 Quality Factor Codes 

 Field or laboratory conditions and equipment 

performance can strongly influence sample 

quality and the accuracy and precision of 

field measurements. Likewise, the storage and 

processing of samples may, on occasion, depart 

from standard procedures because of unusual 

circumstances. These situations must be carefully 

documented to properly analyze, interpret, and 

evaluate the water quality data that result. To 

this end, almost all water quality measurements 

in LTRMP have an associated QF code to 

indicate abnormalities or deviation from standard 

procedure (Section 8.4).

3. Sampling Site Characteristics 

and Conditions

 The features of the sampling site and 

conditions at the time of sampling are important 

for interpreting the collected measurements. 

In stratified random sampling, the physical 

configuration and prevailing conditions at the 

randomly sampled sites can also be aggregated 

across sites within the stratum to characterize 

the sampling stratum or the entire sampling area. 

Sampling site characteristics that are measured 

in LTRMP water quality monitoring include 

water depth, water velocity (speed and direction), 

levels of wave action (sea state), ice and snow 

characteristics, substrate composition, and 

aquatic vegetation (type, density, and coverage). 

Quantitative measures of air temperature, sky 

cover, or wind speed are not collected, but site 

comments are used to note general ambient 

conditions and record unusual circumstances.

3.1 Water Depth

 Vertical position, the third spatial dimension 

of an aquatic system after length (y) and width 

(x), is denoted by the symbol “Z” in limnological 

usage and is measured downward from the water 

surface (Z0). The vertical extent of the water or 

maximum water depth (Zmax) is an important 

feature that affects a host of environmental 

factors, including water velocity, vertical mixing, 

temperature, ice cover, and the distribution 

and abundance of river biota. In the UMRS, 

Zmax is influenced by deposition of sediment, 

scouring, and water level fluctuations. Sediment 

movement during high flow can produce major 

changes in substrate elevation and resultant Zmax. 

Construction or alteration of channel training 

structures and dredging can also change water 

depth. In the UMRS, the greatest values for Zmax

(up to 20 m) are usually found in the main river 

channel.

 Precise determination of water depth in 

backwaters and sloughs is often complicated by 

soft, flocculent bottom sediments that are easily 

disturbed and are not distinct from the overlying 

water.

3.1.1 Definition

 Water depth (Zmax) is the vertical distance 

between the substrate and the free-water surface. 

This differs from bathymetry (as defined in the 

LTRMP) that measures the absolute elevation 

of the substrate above some vertical reference 

(usually mean sea level). The first published 

version of the LTRMP Procedures Manual 

(Lubinski and Rasmussen 1988) defined a 

measurement called water depth (WDP) that is 

the vertical thickness of the liquid layer of water 

between the substrate and the bottom of any 

overlying ice cover. The measurement associated 

with this definition has been renamed available 

water depth (AWD; Section 3.2).

 For ice-cover periods before 1993, WDP (now 

AWD) was calculated in the field by subtracting 

ice thickness from a measure of maximum water 

depth. The maximum water depth (i.e., what is 

now called Zmax) was not recorded in the field, 

but has since been estimated in the database 

by adding 90% of the reported ice depth to the 

reported WDP (now AWD). Since July 1, 1993, 

AWD is no longer calculated in the field, but is 

now calculated in the database by subtracting 

submerged ice thickness (Zsice) from Zmax.
19

3.1.2 Method

 Water depth (Zmax) at a sampling site is 

measured using a marked sounding pole, 

nonstretch sounding line, or a calibrated acoustic 

depth finder. The Zmax is recorded in meters 

with two significant figures (e.g., 3.1 m, 0.12 

m). However, three significant figures may be 

reported for water >1.0 m deep if such precise 

measurements are possible (i.e., through the 

ice) and necessary (e.g., to accurately calculate 

AWD). If measurements or samples are to be 

taken at a site, these are done before the substrate 

is disturbed by mechanical depth sounding. 

Precise measurement of water depth in rough 

water can be difficult, but comparison with a 

relatively fixed reference (i.e., average boat 

waterline) rather than the moving water surface 

can help, and best professional judgment must be 

used. Problems are reported with site comments 

and appropriate QF codes.

 In aquatic habitats deeper than 1 m, Zmax can 

also be measured using a calibrated acoustic 

depth finder or a weighted line. If an acoustic 

sensor is mounted on the boat hull, then the 

depth from the water surface to the mounted 

sensor must be considered (note that this can 

change significantly depending on the weight 

distribution, loading, or operation of the boat). 

A sounding line (nonstretch material) marked at 

10-cm intervals can be used if current velocity 

is low enough to permit sounding with this 

approach and the substrate is firm enough to give 

unambiguous readings. If a sounding weight is 

used, the weight must be of sufficient mass to 

keep the cable vertical. Firmness of the substrate 

can be determined by gently bouncing the 

sounding weight up and down on the substrate.

3.2 Water Depth—Available 

 When ice is present, the fraction of the water 

column available to biota beneath the ice can be 

substantially less than the distance from the freewater surface to the substrate. Generally, this is 

significant when ice completely covers the water 

surface, but is also applicable to other forms of 

ice cover (e.g., large blocks). In LTRMP water 

quality monitoring, information is collected when 

appropriate and possible to evaluate the vertical 

extent of the water column below the ice.

3.2.1 Definition

 This measurement, now abbreviated AWD, 

was called water depth (WDP) in the first 

published version of the LTRMP Procedures 

Manual (Lubinski and Rasmussen 1988). It 

indicates the thickness of the liquid vertical water 

column available for aquatic organisms. When 

ice is present, this is the vertical thickness of the 

water layer between the substrate and the bottom 

of the ice. Because ice in the river is not always 

free-floating, but may be grounded or subjected 

to various buoyant or hydraulic pressures, it is 

not possible to calculate precisely the AWD from 

measurements of total ice thickness (Zice) and 

water depth (Zmax) alone.

3.2.2 Method

 The AWD and water depth (Zmax) are identical 

when ice is not present. When ice is present, 

AWD is determined in three steps:

 a. Water depth (Zmax) is determined as 

described earlier.

 b. Submerged ice thickness (Zsice), the 

distance from the bottom of the ice to the 

free-water surface (in the auger hole), is 

measured (Section 3.8.3). This should not 

be confused with total ice thickness (Zice).

 c. The AWD is calculated (to the nearest 

centimeter) in the database (not in the 

field) by subtracting the submerged ice 

thickness (Zsice) from the water depth 

(Zmax).

3.3 Water Elevation

 Water elevation data are collected in the 

bathymetric survey of LTRMP, but not routinely 

as part of water quality monitoring (Wlosinski 

et al. 1995). Basic information on LTRMP 

bathymetry is provided here for reference. 

 Water elevation is the height of the water 

surface above the National Geodetic Vertical 

Datum. It is not the same as water depth (Zmax), 

which is the vertical thickness of the water 
20 

layer. Water elevation in pooled reaches of the 

UMRS is controlled by dam operations when 

river discharges are low to moderate. The 

relation between water elevation and discharge is 

strongest in upper pool reaches. Water elevations 

at navigation control points may not fluctuate in 

response to changes in discharge under low or 

moderate flow conditions. Immediately above the 

navigation dams on the UMRS, water elevations 

may actually decrease as discharge increases 

and more gates are opened. At high discharges, 

all gates in the dams are opened completely, 

and water elevations are a function of discharge 

volume and river topography. Water elevations 

typically rise in springtime because of snow 

melt and high seasonal rains, decline during the 

summer, rise moderately again during fall rains, 

and drop in the winter.

3.4 Wave Height

 Wind- or vessel-generated waves induce 

shear stress that can cause erosion, sediment 

resuspension, and mixing of the water column. 

These effects can influence water quality and 

aquatic biota (e.g., vegetation). Wave height is 

one index of the energy associated with wave 

action. Maximum wave height can be limited 

by water depth, because when wavelength (the 

distance between wave crests) exceeds about half 

the water depth, the wave begins to drag against 

the bottom and the wave rolls over on itself. The 

height of wind-generated waves is determined by 

wind energy input (velocity and duration), fetch 

(open water distance), and water depth.

3.4.1 Definition

 Wave height is the vertical distance 

(amplitude) between the highest (crest) and 

lowest (trough) point on the wave form. In 

LTRMP water quality monitoring, wave height 

is measured with a variety of equipment for 

differing purposes. It has been conclusively 

demonstrated that wave height cannot be 

precisely and consistently estimated by simple 

visual observations, even by skilled observers 

(U.S. Naval Oceanographic Office 1966). 

Consequently, wave categories from the Beaufort 

Scale (Table 5) are used to report wave heights 

encountered during routine monitoring.

3.4.2 Method

 Wave heights observed during LTRMP 

water quality monitoring are reported using the 

Beaufort wind/sea-state scale.

 Although Beaufort Scale conditions above 

4 should be encountered rarely by monitoring 

teams (especially when samples are being 

collected), the Beaufort scale extends to Force 

17 (four levels above hurricane). This method 

of reporting wave heights in LTRMP was 

implemented on May 19, 1993.

3.5 Water Current Velocity

 The speed of horizontal water movement is a 

primary feature of riverine habitat and strongly 

influences the presence and absence of many 

aquatic species. It influences material transport, 

sedimentation, erosion, the degree of turbulent 

mixing, and the level of abrasion and shear stress 

experienced by aquatic biota. In LTRMP water 

quality monitoring, water current measurements 

Table 5. Beaufort wind/sea-state scale.

Beaufort 

number

Wind speed

m/sec MPH Description

0 0.0B0.2 <1 Calm, like glass

1 0.3B1.5 1B3 Light air, ripples w/o 

crests

2 1.6B3.3 4B7 Light breeze, 

wavelets w/o 

breaking crests

3 3.4B5.4 8B12 Gentle breeze, 

wavelets w/breaking 

crests, scattered 

whitecaps

4 5.5B7.9 13B18 Moderate breeze, 

waves w/numerous 

whitecaps

5 8.0B10.7 19B24 Fresh breeze, 

whitecaps w/spray. 

Too rough for small 

open boats
21

are used to generally assess aquatic conditions 

and to explain or confirm other measurements at 

the sampling site. This measurement suggests the 

general level of turbulent mixing that might be 

expected at the sampling site and the connection 

between the sampling site and nearby areas (e.g., 

tributaries, main channel flows, and upstream 

areas). The routine current measurements made 

in LTRMP water quality monitoring are made 

near the water surface and usually from a boat 

that is not rigidly fixed to the substrate. They 

are not intended to be used in flow volume 

(discharge) calculations.

 In a flowing channel without obstructions, 

current velocity generally decreases in a 

logarithmic fashion from just below the water 

surface to the bottom of the channel. The mean 

velocity for the entire water column is closely 

approximated by the velocity observed at a depth 

equal to about 0.6 of the maximum depth. In 

deep channels moving at high velocity, special 

equipment is needed to accurately (and safely) 

gage velocity at depth. Further, current velocity 

can vary dramatically both spatially (horizontal 

and vertical) and temporally (over time). 

Consequently, spot measurements of current 

velocity at routine sampling sites provide only 

a coarse indication of water movement in the 

vicinity of the site at the time of sampling.

 Because a general indicator of water velocity 

is generally sufficient for the purposes of routine 

LTRMP water quality monitoring, water velocity 

measurements may be reported in velocity 

categories (Section 3.6) when more precise 

measuring equipment is not available.

3.5.1 Definition 

 Velocity is a measurement of both speed and 

direction (a vector). However, the terms “speed” 

and “velocity” are commonly (if incorrectly) 

used interchangeably. The LTRMP water quality 

monitoring includes both scalar components of 

horizontal water movement (speed and direction), 

and in this manual the scalar speed of horizontal 

water movement is referred to as current velocity. 

Current velocity spans a wide range, (0–3 m/sec) 

and is recorded in meters per second using 

two significant figures. Measurement of flow 

direction is described in Section 3.7.

3.5.2 Method

 Velocity can be measured using a float, 

venturi tube, rotating-element, or electromagnetic 

(Faraday effect) device. Floats are not used 

routinely in the LTRMP and can give only a 

rough estimate of surface water velocity. They 

cannot be used if velocity at depth must be 

measured. However, as a backup or emergency 

measure, a float can be any object with slight 

positive buoyancy (a whiffle ball or an orange 

are reliable and inexpensive floats). The float is 

placed in the river so that the middle of its flow 

path is at the point being described. The time it 

takes for the float to traverse a known distance 

(minimum distance = 3 m) is recorded. Times 

from three trials are used to calculate a mean 

time. Surface velocity is calculated from the 

travel time and the distance traversed. Care is 

taken to use trials that are uninterrupted by wind, 

debris, or other surface disturbances.

 Routine current velocity measurements are 

made with an electromagnetic device following 

the manufacturer’s instructions (Appendix D). 

Velocity is recorded from stable readings (no 

significant change over 10 sec) or, in turbulent 

conditions with unstable readings, is calculated 

as the mean of six consecutive readings of 5 sec 

each. Built-in averaging capabilities within the 

instrument are used as appropriate.

 Velocity measurements are taken at the same 

depth as the corresponding water quality sample. 

However, velocity measurements below 0.2 m 

are not taken routinely as part of water quality 

monitoring. 

 The orientation of the sensor is critical 

when using a directional sensor (venturi or 

uni-directional electromagnetic current meter). 

If the sensor is not oriented correctly (i.e., 

facing directly into the current or direction of 

maximum velocity), the reading will be incorrect. 

In turbulent waters, negative velocities may be 

indicated, but this problem can often be corrected 

by increasing the period of averaging (time 

constant).
22 

 Electromagnetic velocity meters generally do 

not require any field calibration. The zero point 

should be checked regularly (each day of use), 

and the meter should be recalibrated once per 

year. Care must be taken to ensure that the sensor 

surfaces on an electromagnetic device are kept 

clean (follow manufacturer’s guidelines) and are 

not scratched.

 Maintenance is performed on the velocity 

meter according to the manufacturer’s 

instructions and is noted in the maintenance log 

book.

3.6 Water Current Velocity Category

 The LTRMP field teams can report flow 

velocities using a categorical scale (Table 6) 

when precision equipment is unavailable 

or inoperative. Flow velocity category 

measurements can be made using any suitable 

floating object. Flow velocity category 

corresponds to one of a series of seven 

logarithmically increasing classes. When this is 

done, a QF code of “C” (category measure) must 

be recorded.

3.7 Water Current Direction

 Flow direction is the second component of 

flow velocity (speed is the first). Information on 

the direction of flow has limited use in routine 

monitoring but may be helpful in detecting 

anomalous conditions (i.e., backflows or 

subsurface currents) or dramatic changes in 

system geometry.

3.7.1 Definition

 Flow direction is the magnetic compass 

direction from which the flow is moving at the 

sampling point. This is the same system as that 

commonly used to report wind velocity. The 

direction of current flow is estimated to the 

nearest 10°.

3.7.2 Method

 A magnetic compass is properly aligned 

with the predominant direction of flow, and the 

heading is noted and recorded to the nearest 10°. 

The direction of flow is not determined at current 

speeds 0.02 m/sec.

3.8 Ice and Snow

 When ice is present, the underwater 

light climate is strongly influenced by the 

characteristics of the ice (thickness, clarity), the 

horizontal extent of ice cover, and the amount 

of snow covering the ice. Ice cover isolates the 

underlying water from gas exchange and the 

effects of wind resuspension. In the absence of 

resuspension, unusually clear water may develop 

under the ice. If the ice itself is transparent 

and lacks thick or complete snow cover, then 

light penetration is often adequate to support 

massive under-ice algal blooms. Dissolved 

oxygen levels of 200% to 300% of saturation 

may occur directly under the ice in such 

conditions. Likewise, a thick and complete snow 

cover can eliminate light penetration, prevent 

photosynthesis, and result in under-ice anoxia 

with subsequent winter kill.

Table 6. Flow velocity classes used in the Long Term Resource 

Monitoring Program.

Flow velocity

 (m/sec) Category Visual indication

0.00–0.02 0 No detectable water 

movement

0.02–0.06 1 Water movement just 

detectable

0.07–0.14 2 Perceptible surface 

wakes

0.15–0.30 3 Estimated from object 

transit time

0.31–0.62 4 Estimated from object 

transit time

0.63–1.26 5 Estimated from object 

transit time

>1.26 6 Estimated from object 

transit time
23

 The presence of ice complicates sampling 

and alters the definition of some depth-related 

measurements (Figure 2). Additional information 

and specific details on under-ice sampling are 

provided in Section 7.5.

3.8.1 Ice—Percent Cover 

 The fraction of the water surface that is 

covered by ice will influence light availability, 

gas exchange (e.g., oxygen, ammonia, carbon 

dioxide), wind mixing, thermal regime, and 

suitability of habitat for aquatic biota. Ice cover 

also affects recreational boating and commercial 

navigation.

3.8.1.1 Definition

 Percent ice cover is a semiquantitative 

estimate of the fraction of water surface covered 

by ice in the vicinity of the sampling point. 

Ice cover in the upstream direction (the source 

of water that flows by the sampling point) is 

of primary interest in this estimate. The ice 

coverage is estimated in increments of 10%.

3.8.1.2 Method 

 Percent ice cover is estimated by visual 

observation around the sampling site. The area 

considered in this assessment corresponds to 

half the grid spacing (i.e., the sampling circle, 

Section 1.7) in stratified random sampling. 

Thus at side channel and contiguous backwater 

sites, ice conditions within a radius of 25 m 

are considered. At all other sites, a radius of 

100 m is applied. If water does not extend to 

the assessment radius in all directions, then the 

water surface within the radius is considered. 

Exposed land and ice that is beached (i.e., laying 

on land that would be exposed at the prevailing 

water level) in the vicinity is not considered. The 

presence of ice in any amount less than 10% is 

reported as 1%.

3.8.2 Ice—Total Thickness

 Total ice thickness (Zice) influences light 

penetration, the potential for ice breakup and 

movement, the extent and chemical composition 

of the underlying water (in isolated backwaters), 

and the suitability of under-ice habitat for aquatic 

organisms.

3.8.2.1 Definition

 Total ice thickness (Zice) is the vertical 

thickness of ice at a defined point. When ice 

extends to or into the underlying substrate, only 

the portion of the frozen block that represents 

the water column is measured and reported. The 

measurement of total ice thickness excludes the 

depth of any water above the ice surface.

3.8.2.2 Method

 The Zice is measured through a hole in the ice. 

A rod or stick marked at centimeter intervals 

and tipped with a right-angle crosspiece (e.g., 

a Secchi disk or 12-cm rod) is used for the 

measurement. The crosspiece is pulled up 

Figure 2. Diagram of various depth (Z) definitions associated with 

ice cover and under-ice sampling. The AWD is available water 

depth, Zbottom is the depth of the near-bottom sample, Zice is the total 

vertical extent of ice, Zmax is the vertical extent of water between 

the substrate and the free surface of the water, Zmid is the depth 

of the mid-depth sample (if required), Zsice is the vertical extent 

of ice below the water surface, and Zsurface is the depth of the 

near-surface sample. Zsurface is always recorded as 0.2 m, regardless 

of ice presence. Thus, in all instances, the actual depth of Zsurface

below the level of the free-water surface is 0.2 m plus Zsice.
24 

against the bottom of the ice, while the rod is 

held vertically and the vertical distance from the 

crosspiece to the upper surface of consolidated 

ice (exclusive of slush, snow cover, or overlying 

water) is noted. Three measurements, separated 

by about 120° in the horizontal, are made to 

reduce errors when irregular ice surfaces or 

artifacts are produced by making the hole. The 

mean of the three measurements is reported in 

centimeters.

3.8.3 Ice—Submerged Thickness

 When ice is present, the vertical distance 

between the substrate and the free surface of 

the water (Zmax) does not accurately reflect 

the vertical thickness of the water column 

available for aquatic organisms. To accurately 

calculate AWD, a measurement of submerged 

ice thickness (Zsice) is subtracted from total 

water depth (Zmax). When the surface of the ice 

is submerged, whether naturally or by weight of 

sampling equipment, etc., Zsice is measured to the 

water surface. This is necessary to get a proper 

calculation of AWD and sample depth (Z).

3.8.3.1 Definition

 When ice is present, the thickness of the 

submerged portion (Zsice) is determined to the 

nearest centimeter by measuring the vertical 

distance between the bottom of the ice and the 

free surface of the water (usually within the auger 

hole, but see below). If the ice cover is perched 

so that the free surface of the water is below the 

bottom of the ice, then submerged ice thickness 

is reported as zero. If the ice cover is submerged 

so that free water is above the ice surface, then 

the thickness of the overlying water layer is 

included in the submerged ice thickness (Zsice).

3.8.3.2 Method 

 The technique is identical to that used for ice 

thickness (see above) except that the upper point 

of measurement is the free surface of the water 

rather than the upper vertical extent of the ice.

3.8.4 Snow Depth

 The depth of snow on top of the ice influences 

light penetration to the surface of the ice and 

the light available to aquatic biota below the ice. 

Because of its insulating properties, accumulation 

of snow over the ice can significantly retard ice 

formation and prevent the water column from 

freezing completely in shallow locations.

3.8.4.1 Definition

 Snow depth is the vertical thickness of snow 

on the ice in the vicinity of the sampling location 

measured to the nearest centimeter.

3.8.4.2 Method

 Snow depth is measured by pushing a 

graduated staff vertically into the snow until 

an abrupt increase in resistance is encountered. 

The end of the staff should have a 6.4-cm2 (1-

inch2) surface area. Three measurements are 

made within 1 m2 to reduce errors from irregular 

snow and ice surfaces. The mean of the three 

measurements is reported in centimeters.

3.8.5 Snow—Percent Cover

 The discussion of snow depth (Section 3.8.4) 

also applies to percent snow cover.

3.8.5.1 Definition

 Percent snow cover is a semiquantitative 

estimate of the fraction of the total horizontal 

surface (water and ice) covered by snow in the 

vicinity of the sampling site. It cannot exceed the 

percent ice cover (i.e., the fraction of the water 

surface covered by ice). 

3.8.5.2 Method

 Percent snow cover is estimated in a manner 

similar to that used for percent ice (i.e., visual 

observation around the sampling site). The 

percent ice cover can be multiplied by the 
25

fraction of ice covered by snow to estimate the 

snow fraction. For example, if percent ice cover 

equals 50% and 70% of the ice is covered by 

snow, then percent snow cover equals 0.5 x 0.70 

= 0.35 or 40% (rounded to the nearest 10%). 

Percent snow cover is reported in increments of 

10%. If the percent snow cover is less than 10% 

but greater than zero, it is reported as 1%.

3.9 Substrate Characteristics

 Sediment dynamics (resuspension, transport, 

deposition, modification) and sediment 

characteristics are central to the functioning 

of the UMRS ecosystem. In addition, the 

effects of human activities (e.g., navigation, 

recreational boating, dredging, agriculture) are 

tied to (and reflected by) the spatial distribution 

of sediment types. Water quality monitoring 

in the LTRMP emphasizes parameters that are 

related to suspended sediment (e.g., turbidity, 

suspended solids, Secchi disk transparency, 

total phosphorus), but detailed information on 

substrate sediment characteristics and the spatial 

distribution of sediments in the UMRS is not 

addressed in water quality monitoring. As part 

of routine water quality monitoring, general 

information on substrate type is collected to 

suggest (1) the prevailing flow regime at the 

sampling site, (2) the nature and extent of the 

bottom sediment influence on water quality in 

the overlying water, and (3) the type and amount 

of biota that might be expected at a specific 

location.

3.9.1 Substrate Particle Size

 Substrate particle size is not measured as 

part of routine water quality monitoring. The 

following information is provided for reference 

only. These categories are modified from 

Wentworth’s classification (Welch 1948) to 

include particles common to UMRS aquatic 

habitats.

3.9.1.1 Method

 The previous version of this manual outlined 

the following methodology: Substrate is collected 

using a sampler appropriate to the situation. 

Variability in substrate types, water depth, and 

current velocity in the UMRS has prevented 

standardization on a single sampler. Either a 

corer or a Ponar sampler is appropriate for most 

situations. In high velocity areas characterized by 

mussels, hard clay, bedrock, or boulders, diving 

may be necessary to adequately identify the true 

substrate particles present. The upper 10 cm 

of the substrate sample is visually inspected 

by a technician trained in the identification of 

substrate particle categories. Table 7 describes 

one method for classifying substrate particles.

3.9.2 Substrate Hardness

 Substrate hardness is not measured in routine 

water quality monitoring, but the following 

information is included for reference. Substrate 

Table 7. Substrate particle categories based on Wentworth’s 

classification (Welch 1948).

Category 

Description or

particle diameter

(mm)

Bedrock None

Boulder >256

Cobble 255B64

Gravel 63B2

Coarse sand 1B0.25

Fine sand 0.24B0.062

Silt 0.061B0.004

Clay <0.004

Detritus Dead plant parts, any size (with 

the exception of woody debris, 

which will be quantified later 

under Afish cover@)

Mussel shells Either live or dead
26 

hardness is widely variable in the UMRS and is 

not a direct function of substrate particle size. 

For example, backwater sediments composed 

primarily of silt can vary considerably in 

hardness depending on their past history of 

exposure to air, the presence of anaerobic 

conditions, aquatic vegetation, and general 

turbulence. Firm silt substrates are likely to 

support more diverse and abundant epibenthic 

and macrobenthic communities than do 

extremely flocculent silts.

3.9.2.1 Method

 Standard methods for determining substrate 

hardness in the LTRMP have not been developed. 

The first published version of the LTRMP 

Procedures Manual (Lubinski and Rasmussen 

1988) called for measurement with a 9.1-kg (20-

lb) weight attached to a disk 20 cm in diameter. 

The disk is suspended at the surface of the 

substrate by a cable graduated in centimeters. 

The disk is released and allowed to penetrate 

the substrate. The depth of the disk is recorded 

at 15-sec intervals until no change in depth is 

observed. The distance in centimeters between 

the final resting depth of the disk and the water 

depth is reported as substrate hardness. Using 

this technique, substrate hardness can only be 

measured in silt-dominated sediments. Other 

methods have been investigated, but none 

adopted for routine use.

3.9.3 Predominant Substrate

 Water quality monitoring in the LTRMP uses 

five categories to record predominant substrate 

type (Table 8).

 Any suitable device for obtaining a surficial 

sample of bottom material can be used to make 

the determination. This measurement is required 

in backwaters only, but at the discretion of 

the field team these measurements can also be 

made in channels. In FSS, measurements of 

predominant substrate are made at least once per 

quarter; they are required in backwaters during 

all SRS episodes.

3.10 Aquatic Vegetation

 A separate component of the LTRMP 

addresses the spatial and temporal distribution 

and abundance of aquatic plants in the UMRS 

and this is described elsewhere (Rogers and 

Owens 1995). Water quality teams in the 

LTRMP only collect rudimentary information 

on aquatic vegetation in the immediate vicinity 

of the sampling site as needed to help interpret 

measurements from the site.

3.10.1 Percent Aquatic Plant Coverage

 

 Four general categories are used to report the 

approximate extent of aquatic plant coverage 

(submergent, emergent, and floating) around 

the sampling site. The area considered in this 

assessment corresponds to half the grid spacing 

(i.e., the sampling circle, Section 1.7) in SRS. 

Thus, at backwater and side channel sites, 

coverage within a radius of 25 m are considered. 

At all other sites, a radius of 100 m is applied.

 0 = No aquatic vegetation visible at the site

 1 = 1–19% coverage of the sampling site with 

aquatic vegetation

 2 = 20–49% coverage

 3 = Greater than 50% coverage 

Table 8. Predominant substrate categories used in the Long Term 

Resource Monitoring Program.

Numeric

code Category Description

0 Clay Hard, without sand or 

organic material

1 Silt Soft, flocculent

2 Silt/clay/

sand

Any mixture of two or 

more of these materials

3 Sand May contain small 

amounts of other 

material

4 Hard Concrete, rock, gravel, 

riprap, etc.

9 Not obtainable Cannot obtain sample
27

3.10.2 Vegetation Density

 Vegetation density is reported in two 

categories, sparse or dense. This subjective 

measure gives an approximate characterization of 

stem or leaf density within the plant bed. 

3.10.3 Vegetation Type

 The LTRMP uses the following five categories 

to record the predominant vegetation growth 

form(s) at a sampling site:

 S = Submergent

 E = Emergent

 F = Floating

 B = Two of the above categories

 C = Combination of S, E, and F

4. Physical and Aggregate Properties 

of Water

 The physical and aggregate properties of water 

are of major importance to the aquatic biota but 

are not gaged directly by the concentrations of 

distinct chemical or biological species. This 

category of measurement includes acidity, 

alkalinity, conductivity, hardness, light extinction, 

density stratification, temperature, turbidity, 

transparency, pH, and suspended solids. Of 

these, routine LTRMP water quality monitoring 

includes conductivity, Secchi disk transparency, 

suspended solids, temperature, turbidity, and pH. 

Photosynthetically active radiation (PAR) is not 

monitored routinely at present in LTRMP water 

quality, but may be added in the future. Vertical 

water density differences (stratification) are not 

measured in the field, but evaluated from vertical 

measurements of temperature and conductivity.

 Although turbidity, Secchi disk transparency, 

and suspended solids are interrelated, all three 

continue to be monitored in the LTRMP water 

quality component. The data collected from 

1993–2001 show that the relations among these 

variables are not precise and can change over 

space and time. With the exception of suspended 

solids (a high priority measure in the LTRMP), 

these measures are quick and easy to obtain and 

provide cross-check and back up if a result is in 

question or missing.

 The instruments used to measure physical 

and aggregate properties of water in the LTRMP 

have evolved over the course of the Program. 

Care has been taken to compare the performance 

of new equipment to existing instruments to 

ensure that artifacts are not introduced into the 

long-term record by instrument replacements. 

Sometimes (e.g., turbidity) the need for longterm consistency has prevented the LTRMP from 

using all the capabilities of newer instruments. 

The equipment used in LTRMP for in situ water 

quality monitoring as of the date of this manual’s 

publication are listed in Appendix E.

4.1 Conductivity 

 Conductivity (the ability of water to conduct 

an electric current) is an aggregate property 

that reflects the total amount of ionic material 

dissolved in the water. Conductivity is useful for 

determining the source and movement of water, 

for gaging the impact of precipitation events, 

for cross-checking the validity of correlated 

measurements, and (sometimes) for estimating 

chemical characteristics that are more difficult to 

measure directly. It is also a major consideration 

in electrofishing efficiency.

4.1.1 Definition

 Conductivity is the ability of a cubic 

centimeter of water (1 cm2 in cross section and 

1 cm in length) to transmit an electric current. 

It is the reciprocal of resistance (ohms) and is 

reported in microseimens per centimeter (μS/cm). 

This unit is exactly equivalent to the micromho 

per centimeter (μmho/cm). Conductivity (also 

called specific conductance) is defined at 25°C 

and measurements made at other temperatures 

must be corrected accordingly. The exact 

correction is dependent upon the precise ionic 

composition of the water, but an approximate 

correction can be made that will bring the result 

within 1–2% of the actual value under most 

circumstances. This approximation is acceptable 

for LTRMP purposes and is performed 
28 

automatically by all conductivity devices used in 

the LTRMP.

4.1.2 Method

 Conductivity measurements are usually 

made in situ as part of a multisensor array, but 

grab samples can be collected and measured 

when measurements in situ are not feasible. 

Grab samples are collected using a suitable 

depth-specific sampler (Section 7.3). Grab 

sample conductivity measurements should 

be made immediately and samples should 

not be stored. The calibration of conductivity 

instruments must be checked at the start and end 

of each day according to the instrument manual 

(Appendix D) by comparison to standards that 

bracket ambient conditions (i.e., 0.002 M and 

0.005 M potassium chloride solutions; APHA 

1992).

 

4.2 pH

 Measurement of pH is one of the most 

important and frequently used measurements 

in water chemistry (APHA 1992). Chemical 

equilibria, biotic processes, and toxicity of 

various constituents (e.g., ammonia) are all 

pH-dependent. Natural waters generally have 

pH values in the range of 4 to 9. The UMRS, 

which is well-buffered, has pH values generally 

above 7 and usually between 6.5 and 8.5. 

Photosynthesis will strongly influence pH, 

and higher pH values can be expected in the 

afternoon, on sunny days, or beneath clear ice in 

association with aquatic vegetation beds or algal 

blooms. See Standard Methods (APHA 1992) for 

additional information. Remember that pH is a 

logarithmic measurement and that each pH unit 

indicates a 10-fold difference in hydrogen ion 

activity. For this reason, pH values should not be 

“averaged” in the same fashion as nonlogarithmic 

measurements. 

4.2.1 Definition

 The pH of a solution is the negative logarithm 

(base 10) of hydrogen ion activity (approximately 

the hydrogen ion concentration). Thus, the 

hydrogen ion activity in a pH 7.0 sample is 

10 times greater than in a pH 8.0 sample. The 

LTRMP measures pH potentiometrically with 

a glass electrode and records it to the nearest 

0.1 unit.

4.2.2 Method

 In LTRMP water quality monitoring, 

pH is generally measured in situ as part of 

a multisensor array (Appendix D). In situ

measurements are required because a pH sample 

cannot be preserved and pH can change rapidly 

and dramatically because of degassing, aeration, 

photosynthesis, or respiration.

4.3 Photosynthetically Active Radiation 

 The PAR is not routinely measured in LTRMP 

water quality monitoring, but the following 

information is provided for reference.

 The photosynthetic activity of plants is related 

to incident radiation between the wavelengths 

of 400 and 700 nm. The penetration of light 

into the water column can be a major factor in 

the presence or absence of aquatic macrophyte 

species, the quantity and composition of 

phytoplankton, and the rate of carbon fixation 

(primary production).

 The PAR is only a fraction of the total light 

that strikes the water surface. Seasonal weather 

patterns (particularly clouds) influence this 

measurement. During low precipitation years 

(less cloud cover), incident PAR may be above 

average and may also be accompanied by lower 

turbidity (greater light penetration).

4.3.1 Definition 

 The PAR is a measure of incident light 

intensity (number of photons per unit time per 

unit area) between the wavelengths of 400 and 

700 nm (it is sometimes called photosynthetic 

photon flux density). The PAR is typically 

measured in units of micromoles of photons 

per second per square meter (μmol s-1 m-2). It 

assesses the light available for plant growth. The 
29

PAR measurements taken at discrete depths are 

used to estimate the extinction coefficient in the 

following equation:

Iz/I0 = exp(-extinction coefficient * z)

where Iz and I0 are the PAR measurements at 

depth (z) and the surface, respectively, and exp is 

the exponential function.

4.3.2 Method 

 At defined locations, PAR is measured above 

the water surface (1 m) and at logarithmic 

increments (e.g., 10, 20, 40, 80, 160, and 

320 cm) below the water surface until the PAR 

is <10 μmol s-1 m-2 or the bottom is encountered. 

It is critical that reflections or shadows from 

the boat and equipment, the field team, and 

the sensor cables themselves do not influence 

measurement. Measurements should be taken 

on the sunny side of the boat. Keep in mind 

that the boat’s shadow, although perhaps not 

visible on the water surface, projects downward 

at an angle below the boat (dependent on the 

position of the sun), and that the sensors can be 

inadvertently lowered into this shadow, if care 

is not taken. Likewise, reflections from the boat 

hull and equipment can influence the readings—

particularly surface or deck cell measurements. 

If a deck cell is used, it should be positioned 

above the boat and equipment. Submerged 

measurements should be taken away from the 

boat as much as practicable (a polyvinyl chloride 

plastic pipe is useful for this purpose).

 The simultaneous use of two sensors (deck 

and submersed cells or two submersed cells) 

is strongly recommended and allows for an 

estimate of light extinction in the water, even 

when sky conditions are variable. Under clear 

sky conditions and for short intervals, dual cells 

are not necessary. Specific LTRMP methods for 

measurement of PAR are not established. The 

LTRMP is using quantum light sensors (LICOR, Inc., Lincoln, NE [previously LAMBA 

Instruments Corporation]) connected to various 

data loggers and the manufacturer’s operating 

and maintenance procedures are followed.

4.4 Secchi Disk Transparency

 Secchi disk transparency is an established 

and convenient limnological index for measuring 

water clarity. It correlates reasonably well 

with turbidity, suspended solids, visual light 

extinction, and light availability for plant growth 

(Cole 1979). When multiplied by a value 

between 2.7 and 3.0, Secchi disk transparency 

roughly indicates the depth at which 1% of the 

surface incident light remains and this depth 

is commonly accepted as the lower boundary 

of the euphotic zone (Cole 1979). Secchi 

disk transparency can be measured easily and 

quickly, can be compared to historical data, and 

can provide a check on other measurements 

such as PAR, turbidity, suspended solids, 

and chlorophyll-a related to water clarity. 

Disadvantages of this method are that it requires 

suitable midday illumination, only surface 

measurements are possible, it is unusable in clear, 

shallow water where the disk is in view while 

resting on the bottom, and it can be difficult or 

impossible to obtain readings in water that is 

rough or moving at velocities greater than a few 

centimeters per second.

4.4.1 Definition

 Secchi disk transparency is the vertical 

distance below the water surface at which a 

Secchi disk disappears from the view of a person 

located directly above the disk. In the LTRMP 

database, Secchi disk transparency is recorded 

in centimeters. The measurement depends on 

the ambient light at the water surface, the light 

attenuation characteristics of the water between 

the disk and the water surface, the roughness of 

the water surface, and the visual acuity of the 

observer.

4.4.2 Method

 Secchi disk values are made with a flat, 

circular plate with alternating black and white 

quadrants. A Secchi disk attached to a cable 

or rigid rod marked at centimeter intervals is 

lowered into the water in the shade of either the 
30 

boat or the observer to avoid glare off the water 

surface. Sunglasses are not worn while making 

this measurement. The distance at which the disk 

disappears is noted, the disk is raised, and the 

depth at which it reappears is noted. The mean 

of these two depths in centimeters is recorded as 

Secchi disk transparency. Various sizes of Secchi 

disk are in common use; the LTRMP generally 

uses a disk with a 20 cm diameter. If necessary, 

any white object that can be raised and lowered 

in a controlled fashion and that has a reasonably 

flat upper surface can be used for Secchi disk 

measurements. If a nonstandard device is 

used, this is so noted using a QF code of “A” 

(nonstandard method used) and an explanation 

provided in the site comments field of the data 

sheet.

 In flowing water, Secchi disk transparency 

measurements require a heavily weighted or 

rigidly mounted disk. Alternatively, the boat 

may be allowed to drift with the moving water to 

ensure that the disk hangs vertically. In situations 

where the Secchi disk can be seen even after 

it comes to rest on the substrate, the depth at 

which the disk comes to rest is recorded and 

an appropriate QF code of “2” (reading offscale, high) is recorded. Before June 12, 1993, 

when the Secchi disk transparency could not be 

directly measured (e.g., disk was visible on the 

bottom), a Secchi disk transparency of -9 was 

recorded. In rough water, accurate Secchi disk 

transparency readings can be nearly impossible 

and best professional judgment must be used to 

estimate the average depths of disappearance and 

appearance of the Secchi disk.

4.4.3 Calibration 

 Secchi disk transparency is an individualized 

measurement and cannot be easily calibrated 

for precise measurement. Observers who are 

accustomed to turbid water will usually report 

greater Secchi disk transparencies under turbid 

conditions than observers who work primarily in 

clear water. The Secchi disk equipment itself is 

calibrated by remeasuring the rope or cable once 

a month to check for shrinkage or stretching. The 

graduated markings are renewed as needed to 

correct for fading, and the Secchi disk itself can 

be repainted.

4.5 Suspended Solids

 As in most large rivers, sediment dynamics 

are a central feature of the ecological structure 

and functioning of the Upper Mississippi River. 

The movement of suspended material (seston) is 

the main determinant of turbidity in the system 

and is the process involved in both erosion and 

sedimentation. The deposition of suspended (and 

bed load) material in backwaters of the Upper 

Mississippi River is considered by many to be the 

most serious threat to habitat and recreation in 

the river, and the processes that affect suspended 

solids concentrations are a major concern in 

evaluating the effects of navigational traffic on 

the UMRS. High levels of suspended solids 

increase the cost of treatment for municipal and 

industrial water supply uses and are aesthetically 

undesirable.

 Because suspended sediment has been 

identified as a high priority measurement for the 

LTRMP, this variable is collected at all sampling 

locations in FSS and SRS.

 Suspended solids (wash load) concentrations 

are generally determined as total dry mass per 

liter (total suspended solids, TSS) and as two 

fractions of the total: (1) nonvolatile (inorganic) 

solids (NVSS), and (2) volatile (organic) 

solids (VSS). The concentration in these two 

fractions is useful in determining or estimating 

the source of the material and other important 

characteristics.

 The nomenclature for material suspended 

in the water has varied with time and across 

disciplines. In limnology, the total of all 

suspended particulate material is called 

seston (Wetzel 2001). In water treatment and 

engineering practice, this same material has 

been called nonfilterable residue, although the 

term suspended solids is now standard (APHA 

1992). Suspended solids, or seston, includes 

organic detritus, phytoplankton, and inorganic 

particulates (e.g., clay, silt, sand).

 Rivers transport variable amounts of highdensity or large-particle sediment along their 
31

beds (bed load) and, thus, the concentration of 

suspended solids taken near the surface may not 

represent the total mass of material transported 

downstream. Nonetheless, suspended solids 

concentration is an accurate measure of the 

fine particulate carried by the channel and is 

appropriate to LTRMP that emphasizes the 

biological effects of transported material and 

relative changes in transport over time, rather 

than total mass. It is also significant that the bulk 

of particle-associated contaminants (including 

phosphorus) in the water are associated with the 

smaller particles that are represented well by 

suspended solids. Further, these finer particles 

near the surface (which includes suspended 

algae) are the primary contributors to turbidity 

that impacts light penetration and water clarity.

4.5.1 Definition

 Suspended solids and the fractions thereof 

(total, inorganic, or fixed, and organic or 

volatile) are defined by the methods used in their 

determination. In LTRMP, the methods described 

in Standard Methods (APHA 1992, 1998) are 

used in these determinations. Note that in some 

earlier editions of Standard Methods, suspended 

solids were called nonfilterable residue. The 

LTRMP follows the practices of the 18th edition 

of Standard Methods (APHA 1992), and total 

particulate material that is trapped by a glassfiber filter (type A/E) disk and dried at 105°C 

is called TSS. This material is then ignited 

(combusted) at 500°C and the residue (ash) that 

remains is called NVSS. This is considered the 

inorganic or mineral fraction of the suspended 

material. Finally, the weight lost during the 

combustion process is called VSS, considered to 

be the organic fraction of the suspended material. 

Particles >2 mm are excluded from suspended 

solids measurements in LTRMP water quality 

monitoring.

4.5.2 Method

 The methods for filter preparation and final 

analyses are detailed in Standard Methods

(APHA 1992). Only the methods for sample 

filtration and handling are addressed here.

 The filtration apparatus is assembled with the 

47-mm glass-fiber filter (type A/E) positioned 

with wrinkled side up. Suction is started and the 

filter is wetted with a small volume of reagentgrade water to seat it. There is no restriction 

specified for the level of vacuum used in this 

suction procedure, but the suction equipment 

used in the LTRMP will generally not produce 

more than 20 inches (65 kPa) of vacuum. 

Sensible limits must always be observed to avoid 

rupturing of the filter or causing other equipment 

failure. In preparation for filtering, the sample is 

agitated in its container vigorously to resuspend 

any material that may have settled. The graduated 

cylinder used to measure the sample volume 

is rinsed first with a small volume of sample 

water before the measurement. After rinsing the 

cylinder, the capped water sample is agitated 

vigorously once more and a suitable volume 

(roughly 50–1,000 mL depending on location, 

season, etc.) of sample is immediately poured 

into the graduated cylinder (type TD). See below 

for guidelines on highly concentrated samples. 

The measured volume is then poured from the 

graduated cylinder onto the seated filter and the 

sample is suctioned to dryness (at least 30 sec 

after filtration looks complete). The funnel is 

then rinsed with at least three small volumes 

of reagent-grade water to move any particles 

clinging to the walls. The filtered sample volume 

(excluding the reagent water used for rinsing) is 

recorded. The damp filter is carefully removed 

from the apparatus and transferred to the storage 

planchet. The filter is positioned in the planchet 

so that the residue on the filter surface does not 

contact the planchet. An appropriate label (bar 

code) is attached to the planchet and it is then 

stored in darkness and frozen until ready for 

shipment to the LTRMP laboratory.

 Several trade-offs must be made in this 

procedure. To maximize analytical accuracy, it 

is important to filter the maximum practicable 

volume, while keeping the total residue 

considerably under 200 mg (a lot!) to avoid 

forming a water-impermeable crust on the filter 

surface. Once the filter has become clogged 

with material, the filtration rate drops abruptly 

and the time required to complete the filtration 

becomes impractical. When dealing with small 
32 

filtration volumes (i.e., 50–100 mL) having high 

concentrations of suspended solids, a precision 

(±1%) pipette (i.e., 25–50 mL) should be used 

to measure out the sample volume instead of a 

graduated cylinder. Care must be taken to ensure 

the sample is vigorously agitated immediately 

before drawing off the sample and that the 

sample is taken from middepth in the container. 

Adding repeated small volumes of sample (i.e., 

20-mL increments) to the filter is generally 

unacceptable because measurement errors 

accumulate with each increment added (this is 

particularly true with graduated cylinders) and 

settling of material in the sample is increasingly 

likely. When repeated volumes must be used, 

precise and accurate (±1%) measuring equipment 

is essential and the number of incremental 

additions should be kept to four or less. Further, 

the sample container MUST be agitated 

vigorously before each subsample is withdrawn. 

If a graduated cylinder is used to deliver a 

single increment of sample and filtration time is 

prolonged (several minutes), then special care 

must be taken to ensure that no material settles 

to the bottom of the graduated cylinder or clings 

to the wall. If TC glassware is used, then a small 

volume of reagent-grade water should be used to 

rinse any material that clings to the cylinder walls 

onto the filter (this volume is not included in the 

reported filtration volume).

 Large particles (>2 mm) are not included 

in suspended solids measurements made by the 

LTRMP water quality teams. This practice may 

exclude some large algal colonies, but these 

large colonial aggregates are not uniformly 

distributed in the water column at the scale 

of LTRMP measurements, they do not arrive 

at the laboratory intact (easily damaged 

by shipping and handling), and they create 

aberrant, nonreproducible results. The LTRMP 

near-surface samples (0.2 m) are specifically 

intended to exclude material floating on the 

water surface and field teams can avoid many 

of these large particulates (e.g., duckweed and 

vegetation fragments) by proper sampling. 

Several methods can also be used to remove 

large pieces of vegetation and other debris from 

the whole water sample before measurement 

and filtration for suspended solids. Passing the 

water through a #10 sieve (2 mm, 0.0787 inch, 

USA standard testing sieve) or equivalent is 

appropriate. Large pieces of vegetation and other 

debris can also be individually plucked from the 

sample container using clean forceps or other 

suitable and clean device, but in most instances 

another sample should be collected. The surface 

of the filter media should be visually examined 

when filtration is complete. If large particulate 

is present, the filter must be discarded. It is not 

acceptable to manually remove particulate from 

the filter surface or from the filtration volume 

after it has been measured. If not enough sample 

volume remains to repeat the filtration and 

replacement sample cannot be obtained (i.e., 

filtration is conducted in the laboratory), then 

the sample is lost and should be appropriately 

flagged (QF code of “5”).

4.6 Temperature—Water

 Temperature is perhaps the most commonly 

measured water quality parameter. It is used 

to correct conductivity, pH, and dissolved 

oxygen measurements in multiparameter field 

instruments and is a critical chemical–biological 

factor that affects a wide range of phenomena, 

such as the presence or absence of species, 

growth rates, the rates of chemical–biological 

reactions, chemical equilibria, and organism 

tolerance to disturbance or stress. Water 

temperature has additional importance as the 

primary contributor to density stratification. 

Water temperature and thermal stratification in 

the UMRS are influenced by solar radiation, 

precipitation, tributary and groundwater inflow, 

and thermal discharges (i.e., from generating 

plants). In general, river temperatures increase 

downstream (north to south) on both the Illinois 

and Mississippi Rivers. Backwaters tend to 

warm more rapidly in the spring and cool more 

rapidly in the fall than do open channels. Shallow 

backwaters also tend to exhibit greater diurnal 

temperature fluctuations and more frequent 

thermal stratification than the main channel.
33

4.6.1 Definition

 Water temperature in LTRMP is defined as 

the in situ reading obtained with a properly 

calibrated thermistor probe and reported in 

degrees Celsius (°C) to the nearest tenth of 

a degree. Thermometers and thermistors 

are checked quarterly against a precision 

thermometer readable to 0.1°C. Calibration is 

checked against two temperature points once a 

year, or whenever a deviation >0.2°C from the 

reference thermometer is observed. Temperature 

sensing instruments used for field measurement 

of water temperature in LTRMP water quality 

monitoring should have a maximum error of 

±0.2°C in the range of 0–40°C and a response 

time of <1 min. For calibration, the thermistor 

reading is compared to a certified temperature 

of a precision thermometer traceable to the 

National Institute of Standards (NIST, formerly 

the National Bureau of Standards). Note the 

checks must be performed at one of the certified 

temperatures provided on the certification chart 

for the reference thermometer because the 

accuracy of intermediate marks on a certified 

thermometer is not guaranteed. Quarterly checks 

of thermistors should include a reference point in 

the 0–5°C range during winter. 

4.6.2 Method

 Temperature measurements in LTRMP are 

generally made with a thermistor probe as part 

of a multisensor array (Appendix D). Although 

any laboratory grade thermometer can suffice 

for surface measurements, a thermistor probe 

is required for temperature measurements at 

depth. Vertical profiles of temperature (0.2 m 

below the surface and 0.2 m above the bottom 

at minimum) are required in areas >0.60 m 

deep with current velocity <0.10 m/sec. If a 

thermometer is used for surface temperature 

measurements, it should have a scale marked 

for every 0.1°C, with markings etched on the 

capillary glass and it should have a metal case to 

prevent breakage. The thermometer or thermistor 

should have a minimal thermal capacity to permit 

rapid equilibration (response time <1 min). A 

mercury thermometer should never be used for 

field measurements. It is strongly recommended 

that mercury thermometers, if used, be limited 

to backup and cross-checking of thermistor 

readings and that a calibrated thermistor be 

used as the primary method for measuring water 

temperatures in the field.

 Good quality thermistors are stable and 

calibration by the operator is not required 

for general field work. However, before such 

equipment is used for the first time in the field, 

the linearity (accuracy) and response time of the 

thermistor is verified by comparison to a certified 

(NIST) thermometer as described on pages 7–9 

of the Hydrolab Performance Manual (Hydrolab 

Corporation 1991b).

4.7 Turbidity

 Turbidity is a measurement of those lightscattering characteristics of water that reduce 

clarity and, thus, affect the light or visual regime 

for aquatic plants and animals (e.g., visual 

predators). Turbidity is caused, or influenced, 

by suspended matter such as clay, silt, finely 

divided organic material, soluble colored organic 

compounds, and plankton and other microscopic 

organisms. Correlation of turbidity with the 

weight concentration of suspended matter is often 

difficult because the light-scattering properties 

of the suspension are influenced by the size, 

shape, and refractive index of the particulates in 

suspension.

 Older (visual) methods of measuring turbidity 

based on the Jackson candle turbidimeter 

(JTU) have been supplanted almost entirely 

by nephelometric techniques that produce 

measurements of nephelometric turbidity units 

(NTU). These two methods are fundamentally 

different, and interconversion between NTU and 

JTU is highly approximate.

 The advantages of using nephelometric 

turbidity in addition to Secchi disk transparency 

as a measure of water clarity are that turbidity 

measurements can be made on samples taken 

from discrete depths, NTU measurements 

are not influenced by ambient light levels, 

and measurement is less dependent on the 

individual observer or operator. Further, Secchi 

disk transparency cannot be measured when 
34 

transparency exceeds the depth of the water 

column.

 From 1988 to 1996, the LTRMP used 

Hach Model 16800 portable nephelometers 

(Hach Company, Loveland, CO) in the field 

for turbidity measurements. This method has 

advantages but also serious drawbacks. The 

primary advantages are that (1) sample storage 

is eliminated, (2) field teams have a realtime indication of conditions, and (3) sample 

processing can be done during travel among 

stations rather than after return to the laboratory. 

The major disadvantages are that (1) repeated 

field calibrations are necessary, which require 

time and cause equipment wear, even if done 

properly; (2) additional hardware is being carried 

into the field (space limitations, increased risk of 

loss, increased wear of equipment); (3) analyses 

are being performed in a marginal environment; 

and (4) the Hach Model 16800 is now obsolete. 

For routine field measurements, the LTRMP 

replaced the Hach Model 16800 with the Hach 

Model 2100P in September 1994. Substantial 

testing was performed to verify that readings 

with the new instrument are consistent with the 

older method in the 0–100 NTU range. Turbidity 

measurements made after September 1, 1996, 

using the Hach Model 16800 are indicated with 

a QF code of “A” (Section 8.4, nonstandard 

method used).

4.7.1 Definition

 Turbidity is measured in the LTRMP using 

the nephelometric method (APHA 1992). This 

technique measures turbidity by the amount of 

light from an incandescent lamp scattered at 

90° to an incident beam. Turbidity is recorded 

as NTU to the nearest whole unit. Turbidity 

measurements made after September 1, 1996, 

using the Hach Model 16800 are indicated with 

a QF code of “A” (Section 8.4, nonstandard 

method used).

4.7.2 Method

 Nephelometric turbidity can be measured 

by processing grab samples of water, by an in 

situ probe, or with a flow-through instrument. 

The LTRMP has not identified a suitable in 

situ device, and so relies on processing of grab 

samples. Grab samples for turbidity are collected 

using the appropriate depth-specific sampler 

(Section 7.3). The LTRMP does not require that 

turbidity measurements be made in the field, 

but turbidity should be measured at the time 

of collection or as soon as practicable to avoid 

changes in sample characteristics that might 

result from particle precipitation, flocculation, 

dissolution, growth, or decomposition. If the 

measurement is delayed, samples are kept from 

freezing, held in the dark at about 4°C, and 

measured within 24 hours of collection. The 

steps for measuring turbidity on a grab sample 

are as follows (consult the manufacturer's user's 

guide for more specific information on use and 

function of the instrument):

 a. A grab sample is collected (Section 7) 

and inspected to ensure that it has not 

been contaminated with bottom sediment 

or contains large debris or vegetation 

fragments. If the bottom sediment has 

been disturbed or the sample is otherwise 

contaminated, then another sample is 

collected, either in an undisturbed section 

of the site or after the water current has 

cleared the disturbance.

 b. The sample should be gently inverted 

several times immediately before 

measurement. This resuspends any settled 

particulates without introducing air 

bubbles into the sample.

 c. The cuvette is rinsed with sample water, 

and then an appropriate volume of sample 

is carefully poured into the clean cuvette. 

Avoid creating air bubbles while 

pouring the sample, and do not handle 

the cuvette in the optical area as oils 

from the skin will cause an erroneous 

reading.

 d. Carefully wipe the cuvette dry with a 

piece of cheesecloth or other soft material 

(laboratory wipes may scratch the glass). 

Periodically apply a thin film of silicone 

oil and wipe with a soft cloth to cover 

glass imperfections. Place cuvette into 

the nephelometer (Hach Model 2100P). 

Maintain a consistent orientation of the 
35

cuvette (i.e., one surface always facing 

forward).

 e. Record the turbidity measurement. If the 

reading is unstable (i.e., fluctuates more 

than ± 5% because of settling of material 

or movement of large particles), use signal 

averaging mode.

 f. Sample dilution is required whenever 

the raw turbidity reading is greater than 

100 NTU. Although the nephelometer 

(Hach Model 2100P) presently used 

in LTRMP can read values higher than 

100 NTU, previous equipment could not. 

Thus, dilution is required to maintain 

consistency with the earlier data. 

Nephelometer readings are recorded 

before (raw instrument reading) and after 

dilution. When samples are returned from 

the field for turbidity measurement, it is 

possible to use precision equipment to 

produce the minimum dilution required by 

the ambient turbidity (Table 9). However, 

when measurements are made in the field 

and a large number of samples require 

dilution, containers with premeasured 

dilution volumes can be prepared up 

to 24 hours in advance of sampling. 

Typically, the same premeasured dilution 

volume (e.g., 25 mL) of analytical grade 

water is dispensed precisely into each 

dilution container. The containers are then 

sealed for transport to the field. In the 

field, a preset sample volume (5.00 mL) 

is precisely dispensed into a preloaded 

dilution container and the sample gently 

mixed. The resultant NTU is determined 

as quickly as possible. The dilution 

factor is determined as in equation (1). 

For example, a premeasured volume 

of 25.00 mL of dilution water and 5 

mL of grab sample results in a dilution 

factor of 6.

Dilution factor = (sample vol. + premeasured

dilution vol.) / (sample vol.) (1)

 Knowledge of field conditions should be 

used whenever possible to guide the selection of 

premeasured dilution volumes. The goal of field 

dilution is to produce a sample in the 30–50 NTU 

range, but clearly this goal will not be achieved 

with premeasured dilution volumes if field 

conditions vary widely or differ greatly from 

expectation. 

 Whenever practical, dilution of turbidity 

samples is performed using a precision pipette 

(e.g., 1–10 mL) for measuring the sample and a 

volumetric flask (20–100 mL) for preparing the 

final dilution. After the sample is added to the 

volumetric flask, reagent grade water is added 

(swirled when about half the water is added and 

then again when three-fourths has been added) 

up to the full volume mark (bottom of meniscus). 

The diluted sample is then poured into a separate 

clean container to ensure good mixing and 

finally is dispensed (poured) into the cuvette for 

measurement. Care is taken when transferring 

samples to avoid the introduction of air bubbles. 

The diluted sample is read in the nephelometer as 

usual, with the dilution factor applied to calculate 

the NTU (e.g., 30 NTU in a diluted sample with 

a dilution factor of 6 is reported as 180 NTU). 

The dilution factor is calculated and applied 

automatically to the diluted sample reading 

when using the electronic data sheet software 

(Section 8.5).

 Each diluted sample is read immediately after 

it is prepared. A batch of diluted samples should 

not be prepared and then read in sequence.

 Repeated dilution or spiking of a diluted 

sample is not permitted. If turbidity is outside the 

desired range after dilution, the diluted sample 

Table 9. Recommended dilution volumes for turbidity samples 

greater than 100 nephelometric turbidity units (NTU). The objective 

of dilution is to bring the instrument reading into the 30B50 NTU 

range.

NTU 

 Sample (mL) 

volume per 100 mL 

total volume

Dilution

 factor

100B200 25 4

201B500 10 10

501B1,000 5 20

1,001B2,500 2 50

2,501B5,000 1 100
36 

is discarded and a completely new dilution is 

prepared.

 The sample and dilution volumes (i.e., 5 + 25) 

are recorded in the sample comment (done 

automatically by ScanLog32). Keep in mind 

that dilution can alter the particles in the sample 

(e.g., by dissolution or precipitation), so dilution 

should be kept to a minimum.

 When dilution is used to produce a final 

turbidity reading, a QF code of “8” (sample 

diluted) is applied to the final turbidity reading, 

but not to the raw instrument reading. A QF 

code of “8” assigned to a raw instrument reading 

indicates that the raw value was off-scale high 

(i.e., >1,000 NTU) and could not be read without 

dilution. The QF code of “8” takes priority over 

a QF code of “4” (sample returned to laboratory) 

that is not required for turbidity samples because 

these are routinely returned to the laboratory for 

analysis.

 Near-surface (0.2-m) nephelometric 

turbidity measurements are made at all sites. 

Measurements at other depths may be required 

if density stratification is present or in situ depth 

profiles are being recorded (Section 7.4).

4.8 Vertical Density Stratification

 Density stratification is a critical feature of 

the aquatic environment and it affects a wide 

range of water quality characteristics. In most 

natural lakes (and many UMRS backwaters), 

density stratification is a seasonal or transient 

phenomenon that is produced most often by 

surface heating of the water. However, other 

processes can produce this phenomenon. For 

example, tributary inflows or groundwater may 

differ substantially from the main body of the 

river (or backwater) in temperature or in the 

amount of suspended or dissolved materials they 

carry. As a result, the density of the inflow will 

not match that of the main body, and density 

layering (stratification) will result. Because water 

density can be altered by dissolved or suspended 

material, stratification may exist even when 

the temperature is nearly uniform from top to 

bottom in the water column, and temperature 

inversions are indeed possible. This is sometimes 

accompanied by unusual subsurface currents 

(e.g., flowing in a different direction or different 

velocity from the surface current). Unusual 

vertical profiles of temperature, dissolved 

oxygen, and conductivity may also be observed 

in the vicinity of groundwater inflows. Velocity 

measurements at depth can sometimes be 

useful in diagnosing such situations in the field. 

Whenever unexpected (e.g., inverted) profiles 

are observed, they should be noted in the site 

comments.

 Water quality monitoring in the LTRMP 

records the presence of density stratification 

because of its ecological significance and because 

procedures must be adjusted to obtain suitable 

representative samples when the water column is 

stratified.

4.8.1 Definition

 Vertical density stratification is defined by 

the vertical rate of change in density in the water 

column. The density gradient can be estimated 

from vertical profiles of water temperature, but 

large vertical changes in dissolved or suspended 

material can interfere with this estimate.

4.8.2 Method

 Vertical density stratification is evaluated 

during routine monitoring by examining the 

vertical profile of temperature, dissolved oxygen, 

and conductivity. Requirements for sampling in 

vertically stratified conditions are presented in 

Section 7.4. 

5. Concentration of Chemical Constituents

 The concentrations of chemical constituents 

in the water are important in determining its 

suitability for aquatic organisms and human use. 

The chemical composition of river water reflects 

inputs from upstream, the biotic and chemical 

activity within the water column, and interactions 

among the water column, underlying substrate, 

and the atmosphere. This section details LTRMP 

methods for collecting and processing samples 

for chemical analysis. Except for dissolved 

oxygen, measured in situ, chemical analyses 
37

are performed in the LTRMP laboratory using 

samples shipped from the field. Laboratory 

procedures used for the analyses are documented 

elsewhere.

 Chemical constituents monitored routinely 

by the LTRMP have included dissolved oxygen, 

plant nutrients (phosphorus, nitrogen, and 

silica), chloride, sulfate, and selected cations 

(calcium, iron, magnesium, manganese, 

potassium, and sodium). Iron and manganese 

measurements were discontinued in February 

1993 (Appendix A, Table A-2). Alkalinity has 

been recommended for inclusion in the LTRMP 

parameter list since 1991 as an important, 

fundamental water quality measure, but addition 

of this measurement has been deemed impractical 

and resources have never been allocated for 

implementation.

 The constituents measured and the frequency 

of measurement in the LTRMP have varied over 

time (Appendix A). Additional characteristics 

(e.g., temperature, pH, conductivity, and 

turbidity) are described in Section 4. Individual 

chemical constituents are arranged alphabetically 

in the sections that follow. 

5.1 Chloride

 Chloride is one of the major anions in 

freshwater and because dissolved chloride 

is nonreactive (conservative), it can be used 

as a tracer of water masses and as a check in 

mass-balance or flux calculations. Chloride 

measurements (in combination with alkalinity 

and sulfate) are also important for determining 

an ion balance for laboratory QA/QC purposes. 

Increases in chloride can sometimes be 

associated with snow and ice removal operations 

on highways within the watershed, or with the 

proximity of wastewater outfalls. Concentrations 

of chloride usually found in the UMRS will not 

directly affect aquatic biota, but increasing levels 

may indicate a change in this situation.

5.1.1 Definition

 Beginning in January 1994, dissolved chloride 

in LTRMP was measured on a filtered sample 

according to Standard Methods (APHA 1992) 

using ion chromatography. It is reported in units 

of mg/L as elemental chlorine.

5.1.2 Sample Collection and Preservation

 An appropriate depth-discrete water sample 

(Sections 7.3 and 7.4) is collected. The sample 

is filtered (0.45-μm membrane; Section 7.8.1) in 

the field (same sample is used for soluble reactive 

phosphorus) and held on ice (approximately 

4°C), until frozen within 24 hours of collection 

for shipment to the laboratory for analysis.

5.2 Metal Cations (Calcium, Iron, Magnesium, 

Manganese, Potassium, and Sodium)

 The dissolved metal cations analyzed by 

LTRMP are important in several ways. Calcium 

is the major cation in the UMRS followed by 

sodium; calcium’s concentration is related to 

the buffering capacity of the water and can 

provide an indication of water source. Iron and 

manganese, although not measured by LTRMP 

at present, are important indicators of anoxia and 

can complex with phosphorus. Potassium is a 

significant minor plant nutrient and can influence 

the distribution of molluscs (Imlay 1973). Further 

discussion of these elements is provided in Cole 

(1979), Wetzel (2001), and Standard Methods

(APHA 1992). Significant quantities of these 

constituents may be associated with particles, but 

the LTRMP only measures the dissolved phase 

(operationally defined by filtration and may 

include colloidal material) as encountered at the 

time of sample collection. Cation samples are not 

digested in the LTRMP, and this precludes the 

determination of total suspended cations.

5.2.1 Definition

 Metal cations are determined on filtered (0.45-

μm membrane) samples that have been preserved 

with nitric acid. Atomic absorption spectrometry 

and ion chromatography are used for analysis 

(APHA 1992). Analytical results for metals are 

reported as elemental concentrations in mg/L. 
38 

5.2.2 Sample Collection and Preservation

 An appropriate depth-discrete water sample 

is collected (Section 7.3). The sample is filtered 

(0.45-μm membrane) in the field, preserved with 

reagent grade nitric acid (Section 7.81), and is 

held in the dark on ice (approximately 4°C), until 

shipped to the laboratory for analysis.

5.3 Nitrogen—Ammonia plus Ammonium

 Ammonia in water is a form of nitrogen 

readily usable by plants that can promote the 

growth of algae and aquatic macrophytes. 

This constituent is present in dissociated and 

undissociated forms in water. As pH increases, 

the equilibrium between these two forms shifts to 

the undissociated form and at elevated pH (i.e., 

above about 8), ammonia is present primarily in 

the NH4OH form (nonionized, undissociated), 

which is highly toxic to aquatic biota (Wetzel 

2001).

 Accurate measurement of ammonia at low 

concentrations in ambient water samples is 

difficult. Ammonia is highly soluble in water and 

a filtered sample is used for the determination. 

However, ammonia is strongly sorbed to 

particles, and the filtration process may remove 

a significant fraction of the total in turbid 

waters. The partitioning between nonionized or 

undissociated and ionized forms of ammonia 

is dependent upon pH and temperature, but 

in the analytical procedure, both ionized and 

undissociated ammonia in the original sample are 

combined and detected colorimetrically. Because 

ammonia gas (NH3) can form and escape from 

the sample at higher pH, the sample is acidified 

immediately after collection to prevent loss to 

the gas phase before analysis. This preservation 

step also halts nitrification (biological oxidation 

of ammonia to nitrate), but unfortunately it also 

encourages ammonia gas from the atmosphere 

to accumulate in the preserved sample. The 

relative portions of dissociated and undissociated 

ammonia in the original sample can be calculated 

from the total ammonia determined in the 

analysis if the ambient pH and temperature of the 

water at the time of collection are known.

5.3.1 Definition

 Ammonia nitrogen is defined as the total 

amount of ammonia (expressed as milligrams of 

elemental nitrogen per liter) that is detected in 

an acid preserved, filtered (0.45-μm membrane) 

sample using an automated phenate method 

(APHA 1992).

5.3.2 Sample Collection and Preservation 

 An appropriate depth-discrete water sample 

is collected (Sections 7.3 and 7.4). The sample 

is filtered (0.45-μm membrane) in the field 

immediately after collection and preserved 

with sulfuric acid (pH approximately 2.5; 

Section 7.8.1) and is held in the dark on ice 

(approximately 4°C), until shipped to the 

laboratory for analysis.

5.4 Nitrogen—Nitrate Plus Nitrite

 Nitrate (NO3) and nitrite (NO2) are highly 

soluble forms of nitrogen in water and a filtered 

sample is used for the determination. In the 

analytical procedure, nitrate is reduced to nitrite, 

which can be detected colorimetrically. Any 

nitrite present in the original sample is also 

detected, so that the result (NOx) is the sum of 

both NO3 and NO2 in the sample. If desired, a 

separate determination on an unreduced sample 

can be used to determine NO2, and NO3 can then 

be calculated by the difference between NOx and 

NO2.

5.4.1 Definition

 The NOx is defined as the total amount of 

nitrite (expressed as milligrams of elemental 

nitrogen per liter) that is detected after a filtered 

(0.45-μm membrane) sample is reduced using 

a cadmium catalyst (APHA 1992). Thus, it 

includes both nitrate and nitrite present in the 

original sample. In the 1990s, LTRMP used 

differing laboratories and analytical methods 

for this determination (Appendix A). Ion 

chromatography of oxidized samples was the 

primary technique used for NOx determination 
39

in the LTRMP from June 1994 through April 

1997 (Appendix A). Ion chromatography is still 

used on selected samples to cross-check the NOx

results from the cadmium reduction method.

5.4.2 Sample Collection and Preservation 

 An appropriate depth-discrete water sample 

(Section 7.3) is collected. The sample is filtered 

(0.45-μm membrane), preserved with sulfuric 

acid (pH approximately 2.5; Section 7.8.1), and 

is held in the dark on ice (approximately 4°C), 

until shipped to the laboratory for analysis.

5.5 Nitrogen—Total

 Nitrogen is a critical plant nutrient and 

component of aquatic organisms that occurs 

in various physical and chemical forms in 

the water column. The operationally defined 

total concentration of nitrogen includes all 

common chemical forms of this element, both 

particulate and dissolved. Because nitrogen 

occurs in both reduced and oxidized states, 

independent analytical pathways have been used 

traditionally to measure reduced and oxidized 

nitrogen compounds. With this approach, total 

concentration is calculated as the sum of the 

two separate analyses. In recent years, digestion 

procedures have been published (APHA 1998) 

that use persulfate to oxidize all common forms 

of reduced and oxidized nitrogen to nitrate, 

requiring only a single analysis. This single 

digestion procedure has gained wide acceptance 

and is used by LTRMP for the determination of 

total nitrogen.

5.5.1 Definition

 Total nitrogen concentration is determined 

using an automated cadmium reduction method 

on a whole water sample following persulfate 

digestion (APHA 1992). 

5.5.2 Sample Collection and Preservation

 An appropriate depth-discrete, whole water 

sample (Section 7.3) is collected. The sample is 

preserved with sulfuric acid (pH approximately 

2.5; Section 7.8.1) and is held in the dark on 

ice (approximately 4°C), until shipped to the 

laboratory for analysis.

5.6 Oxygen—Dissolved

 Dissolved oxygen is a major determinant 

of habitat suitability for many aquatic species. 

The concentration of dissolved oxygen is 

dependent upon exchange with the atmosphere, 

photosynthesis, respiration, and various chemical 

reactions.

 The solubility of oxygen in water (saturation 

concentration) is strongly dependent upon 

temperature, pressure (atmospheric and water), 

and dissolved ions. Of these three factors, water 

temperature has the greatest influence. As 

temperature rises from 0 to 30°C, the solubility 

of oxygen decreases by almost half (14.6-7.6 mg/

L). Atmospheric pressure has far less effect; 

over the normal range that might be encountered 

(720–780 mm/Hg), solubility is increased by 

only 10%. The effects of dissolved material on 

oxygen solubility in the UMRS are generally 

negligible. 

 The dissolved oxygen concentration can 

be a critical habitat feature in shallow areas 

where high water temperatures, ice cover, or 

rapid respiration can result in dissolved oxygen 

levels below 5.0 mg/L (a commonly accepted 

minimum requirement for healthy aquatic biota). 

Inflows from groundwater and tributaries can 

also produce low oxygen levels. Large diurnal 

(24-hour) fluctuations of dissolved oxygen 

are common in highly productive areas (e.g., 

macrophyte beds and algal blooms).

 An assortment of methods are available for 

measuring dissolved oxygen An electrometric 

(amperometric) membrane method (temperature 

compensated) is used in the LTRMP. A number 

of methods are also available for calibrating 

dissolved oxygen sensors (e.g., U.S. Geological 

Survey 1999), and calibration methods for 

dissolved oxygen measurements in the LTRMP 

have evolved over time. An iodometric method 

(azide modification to the Winkler Method) used 

widely for cross-check and calibration of the 

electrometric technique was used by LTRMP 
40 

before July 1997, but this involves the use of 

hazardous materials (sodium azide, concentrated 

sulfuric acid, and concentrated sodium 

hydroxide) and was discontinued (Appendix F). 

Complete discussions of the electrometric and 

iodometric approaches to oxygen measurement 

are available (Wetzel and Likens 1991; APHA 

1992, U.S. Geological Survey 1999).

5.6.1 Definition 

 The dissolved oxygen concentration (mg/L) 

in the LTRMP is determined by an electrometric 

(amperometric) membrane method adjusted for 

temperature and ambient atmospheric pressure. 

The measuring instrument is calibrated in an 

air-saturated water bath (at stable pressure and 

temperature), or more commonly in a watersaturated air chamber. Before 1993, various 

methods were used in LTRMP water quality 

monitoring to indicate dissolved oxygen levels 

that exceeded the upper detection limit of the 

monitoring instrument. For example, values 

>20 mg/L were recorded as either 21 or -9 mg/L. 

This coding scheme is unacceptable because 

valid oxygen concentrations >21 cannot be 

distinguished from over-range values. As of 

August 27, 1993, over-range values are reported 

as the maximum limit of the device and the overrange condition is indicated by a QF code of “2” 

(reading off-scale, high; Section 8.4).

5.6.2 Method

 In the LTRMP, dissolved oxygen and water 

temperature are measured simultaneously in the 

field at the sampling depth. The instrument used 

for dissolved oxygen determination must meet or 

exceed the following requirements:

 a. Suitable precision (i.e., standard 

deviation of five repeated measures on 

a homogenous water sample must be 

<0.1 mg/L) and accuracy (±0.2 mg/L).

 b. Response time and sensitivity specified by 

the manufacturer.

 c. The measurements must be appropriately 

compensated for temperature effects on 

the sensor. Temperature measurements 

provided by the compensating thermistor 

are verified quarterly against an NIST 

traceable thermometer (Section 4.6).

 Performance in each of the above criteria 

is checked at least quarterly. An equipment 

maintenance log verifying the performance is 

maintained for each instrument. Maintenance is 

performed as recommended by the manufacturer. 

This maintenance is documented in the 

instrument maintenance sheet (Appendix J).

 The dissolved oxygen is measured in situ. 

The manufacturer’s recommendations regarding 

daily calibration and use of the equipment 

(including stirrer requirements) are observed 

as described in general guidelines that follow 

(also see Appendix D). A mechanical stirrer is 

generally required for polarographic type probes 

(e.g., Hydrolab [with standard membrane] and 

Yellow Springs Instruments) because this method 

of detection consumes oxygen and vigorous 

water movement over the membrane is needed 

to balance this consumption and obtain a precise 

and accurate measurement.

5.6.3 General Guidelines

 All dissolved oxygen meters and sensors 

should be protected from physical shock and 

extreme heat or cold. Extra care is needed 

when taking dissolved oxygen measurements in 

the winter. The instrument probe(s) should be 

kept in a heated container to prevent freezing 

(Appendix G).

 If the membrane is changed, it should not be 

used for at least 8 hours and preferably allowed 

to equilibrate overnight. If used before that time, 

frequent (i.e., hourly) calibration is needed to 

check for instrument drift.

 The requirements for mechanical stirring 

across the face of the membrane must be closely 

observed. In turbulent water, additional stirring 

may not be necessary, but this must be verified 

(i.e., by observing no change in dissolved 

oxygen during additional stirring or agitation 

of the probe). Mechanical stirring is almost 

always required to obtain an accurate reading in 

quiescent waters. If mechanical stirring is not 

provided with the instrument, then the effect of 

this on dissolved oxygen measurements must be 

verified by comparison to a sensor equipped with 
41

a stirrer. The data from this comparison must 

be properly recorded and made available to the 

water quality coordinator before such equipment 

is used for LTRMP monitoring.

 Some polarographic probes (e.g., Hydrolab 

Datasonde3®) can be continuously powered 

(polarized) to allow rapid equilibration and 

measurement when the full unit is powered up. 

Polarizing batteries are not used routinely in 

LTRMP water quality monitoring, but if these 

batteries are installed, the membrane should be 

removed, the cell drained of electrolyte, and 

a fresh membrane placed over the empty cell 

whenever the unit will not be used for 10 days 

or more. This is necessary to prolong electrode 

life. Before the unit is returned to service, the 

electrolyte and membrane are replaced and the 

new membrane is allowed to “relax” by soaking 

in tap water for at least 8 hours (preferably 

overnight) before use.

5.7 Phosphorus—Soluble Reactive

 The soluble reactive fraction of phosphorus 

includes all chemical forms of the material that 

pass through a 0.45-μm membrane filter and, 

without prior chemical digestion, react with the 

reagents in the detection procedure. The SRP 

(also called dissolved reactive phosphorus) 

was once reported as orthophosphate, but it 

has been recognized that numerous reactive 

chemical forms of phosphorus (in addition to 

orthophosphate) can be hydrolyzed during the 

analysis and will behave as orthophosphate. 

A large majority (if not all) of the phosphorus 

detected as SRP is suitable for immediate uptake 

by bacteria, algae, and aquatic macrophytes. 

Before 1994, true SRP was not measured by 

LTRMP because filtered samples were preserved 

with dilute sulfuric acid, which hydrolyzes some 

portion of the otherwise nonreactive phosphorus 

species. Although preliminary tests have shown 

that the error introduced by this procedure is not 

great (<10%), data obtained from acid preserved 

samples are designated in the LTRMP database 

as soluble reactive phosphorus after hydrolysis 

(SRPH) by acid preservative.

5.7.1 Definition

 The SRP is defined as the total amount of 

reactive phosphorus (expressed as milligrams 

of elemental phosphorus per liter) that is 

detected when a filtered (0.45-μm membrane), 

nonacidified sample is analyzed with the 

ascorbic acid method (APHA 1992). Selected 

SRP samples are cross-checked in the analytical 

laboratory by running a parallel determination of 

orthophosphate on the ion chromatograph. This 

check is only approximate as SRP is not identical 

to orthophosphate.

5.7.2 Sample Collection and Preservation

 An appropriate depth-discrete sample 

(Section 7.3) is immediately filtered through a 

0.45-μm membrane (glass-fiber prefilter allowed; 

Section 7.8.1). It is recommended that SRP 

samples not be preserved (APHA 1992). But 

if analysis must be delayed, Standard Methods

(APHA 1992) recommends that SRP samples 

be frozen after the addition of mercuric chloride 

(HgCl2). In the LTRMP before January 1, 1994, 

SRP samples were preserved with sulfuric acid 

(pH <3) and held in the dark at approximately 

4°C until shipped for analysis. Results obtained 

with this technique are recorded as SRPH (see 

above). After December 1993, LTRMP has held 

samples for SRP analysis by freezing at -10°C or 

colder and without the addition of HgCl2.

 Filtration membranes and glass-fiber filters 

can contribute significant amounts of SRP, and 

Standard Methods (APHA 1992) recommends 

that the filtration media be presoaked in 

laboratory grade water before use. Presoaking 

is not practical with LTRMP equipment and 

to avoid this interference, the first 1–10 mL 

of sample passed through the membrane or 

glass-fiber filter are discarded. In addition, the 

analytical laboratory conducts periodic (biannual) 

tests to evaluate the contribution of filter media to 

the analytical blank.
42 

5.8 Phosphorus—Total

 Phosphorus is a critical plant nutrient that 

occurs in various physical and chemical forms 

in the water column. The operationally defined 

total concentration of phosphorus includes all 

common chemical forms of the material, both 

particulate and dissolved. A single chemical 

digestion can dissolve and hydrolyze all common 

forms of phosphorus in an unfiltered sample 

to produce orthophosphate, which can then be 

measured precisely in a single chemical analysis.

5.8.1 Definition

 Total phosphorus is defined as the total 

amount of reactive phosphorus (expressed as 

milligrams of elemental phosphorus per liter) that 

is detected using the ascorbic acid method after 

an unfiltered sample is digested with persulfate 

under acid conditions (APHA 1992).

5.8.2 Sample Collection and Preservation 

 An appropriate depth-discrete water sample 

(Sections 7.3 and 7.4) is collected. The sample is 

preserved with sulfuric acid (pH approximately 

2.5; Section 7.8.1) and is held in the dark on 

ice (approximately 4°C), until shipped to the 

laboratory for analysis.

5.9 Silica—Dissolved

 Silicon ranks second to oxygen in 

abundance in the Earth’s crust. It appears as 

the oxide (silica) in quartz and sand and is 

combined with metals as complex silicate 

minerals. Degradation of silicate rocks results in 

silica in natural waters as suspended particles, 

colloidal or polymeric silica, and as silicic acids 

or silicate ions. For industrial uses, silica in the 

water is undesirable, but it is an essential nutrient 

required by diatoms, microscopic algae which 

frequently dominate the algal flora of flowing 

waters. Lack of silica can limit the growth of 

these algae, and strong correlations have been 

demonstrated between silica concentration and 

diatom abundance (Wetzel 2001) . 

5.9.1 Definition

 Dissolved silica is defined as the total amount 

of silicate (expressed as milligrams of elemental 

silicon per liter) in a filtered, unpreserved sample 

that reacts using the molybdate method (APHA 

1992).

5.9.2 Sample Collection and Preservation

 An appropriate depth-discrete water sample 

(Sections 7.3 and 7.4) is collected. The sample 

is filtered immediately in the field (0.45-μm 

membrane), but not preserved (Section 7.8.1). 

Silica samples are held in a plastic container 

to prevent contamination by glass (a silica 

compound). Because silicates will precipitate 

under acidic conditions, acid preservatives cannot 

be used. The filtered sample is held in the dark 

on ice (approximately 4°C), until frozen for 

shipment to the laboratory for analysis. Silica 

analyses are normally performed on the same 

sample collected for SRP and chloride analyses.

5.10 Sulfate—Dissolved 

 Sulfate is an abundant anion in waters of the 

Upper Mississippi River Basin. Its concentration, 

in combination with other cations and anions, 

can be used to identify water masses. In anerobic 

conditions, sulfate can replace oxygen as an 

electron acceptor in bacterial metabolism 

and is reduced to sulfide (a toxic substance). 

Because this is a major dissolved constituent, 

the concentration of sulfate is important for 

determining ion balance, an aspect of laboratory 

QA/QC.

5.10.1 Definition

 Beginning in January 1994, dissolved sulfate 

in LTRMP was measured on a filtered sample 

according to Standard Methods (APHA 1992) 
43

using ion chromatography. It is reported in units 

of mg/L as sulfate (SO4).

5.10.2 Sample Collection and Preservation

 An appropriate depth-discrete water sample 

(Sections 7.3 and 7.4) is collected. The sample 

is filtered (0.45-μm membrane, Section 7.8.1) in 

the field (same sample is used for chloride and 

soluble reactive phosphorus) and held on ice 

(approximately 4°C), until frozen for shipment to 

the laboratory for analysis.

6. Biological Measurements

 The abundance and composition of aquatic 

communities in the UMRS is of central concern 

to the LTRMP. The limnological characteristics 

(water quality) of the system can help to explain 

and predict the condition of the aquatic biota, 

and conversely, the condition of the aquatic biota 

can help to explain or interpret the results of 

other limnological measurements. In the LTRMP, 

detailed examination of biological communities 

in the system is largely the responsibility of 

other Program components (fish, vegetation, and 

invertebrates). However, water quality monitoring 

includes selected biological characteristics 

related to the plankton.

6.1 Phytopigments (Chlorophyll-a 

and Phaeophytin) 

 Phytoplankton (suspended algae) are a major 

food source for filter-feeding organisms (i.e., 

mussels, various macro- and microinvertebrates, 

and some fish) in the river. These microscopic 

organisms process nutrients and other materials 

suspended or dissolved in the water, generate 

oxygen during daylight, and can form nuisance 

concentrations (blooms) that can negatively affect 

river biota and interfere with multiple uses of 

the resource (e.g., water supply and recreation). 

The biomass of suspended algae is indicated by 

the concentration of photosynthetic pigments 

(e.g., chlorophyll-a) in the water. The most 

common degradation product of chlorophyll-a is 

phaeophytin, and although this decay product can 

interfere with the chlorophyll-a determination, 

simple steps can be taken to circumvent this 

interference. Phaeophytin has been suggested 

as a measure (negative) of algal “health,” 

but may only indicate the amount of detrital 

material suspended in the water. Techniques 

more advanced than those used in the LTRMP 

are now available to quantify the broad range 

of phytopigments (and taxonomic composition 

of the suspended algae) in a sample (e.g., high 

performance liquid chromatography [HPLC]), 

but simple spectrophotometric or fluorometric 

measurement of chlorophyll-a is rapid, 

inexpensive, and widely used as an indicator of 

phytoplankton biomass.

 Because the mass of suspended algae in 

the main stem and tributaries of the UMR is 

of fundamental importance to the ecology and 

management of this highly enriched system, 

fluorometric chlorophyll-a measurements are 

made at all sampling locations in FSS and SRS.

6.1.1 Definition

 Two types of chlorophyll-a determination 

are used in the LTRMP and the results of these 

two determinations are reported as separate 

parameters. The spectrophotometric method 

for chlorophyll-a uses extraction of a filtered 

sample with 90% buffered acetone and is a 

well-established standard (APHA 1992) in wide 

use for more than 50 years. The chlorophyll-a

obtained with this technique is termed CHLS 

in the LTRMP. The CHLS method is labor 

intensive and has a high detection limit when 

used in turbid waters (because of practical limits 

on filtration volumes), so the LTRMP also uses 

a flurometric determination of chlorophyll-a 

conducted on a filtered sample extracted with a 

50:50 mixture of dimethyl sulfoxide (DMSO) 

and acetone. The result of this method is termed 

CHLF. The CHLF is rapid and easily completed 

with a minimum of sample handling. It has been 

used at all FSS sites since September 16, 1998, 

and at all SRS sites since 1993. Samples are still 

collected for CHLS at a minimum of 10% of all 

sites (all QA/QC sites plus additional sites during 

SRS) to use for later calibration of the CHLF 

values.
44 

6.1.2 Sample Collection and Preservation

 An appropriate depth-discrete water sample 

(Sections 7.3 and 7.4) is collected in an opaque 

container (an amber plastic bottle with 2-L 

capacity is recommended for CHLS). The sample 

is not preserved (Section 7.8.1), but is held 

in the dark on ice (approximately 4°C), until 

filtered onto a glass-fiber filter. Filtration may be 

completed in the field under shade immediately 

after collection, or in the laboratory under 

subdued lighting within 24 hours. Following 

filtration, the filters are kept frozen in the dark 

until shipment to the UMESC laboratory for 

analysis.

6.1.2.1 Method—Spectrophotometric Chlorophyll 

Filtration 

 The filtration procedures for chlorophyll 

determinations are similar to those previously 

described for suspended solids analysis (Section 

4.5.2), except that strict adherence to vacuum 

levels must be followed (suction not to exceed 

0.3 atmospheres, 225–250 mm of Hg, or 5 psi), 

and filtration must be completed in subdued light. 

Even brief exposure to light can alter chlorophyll 

values. The limitation on filtration pressure 

serves two purposes. First and foremost, the goal 

is to avoid the rupture of phytoplankton cells 

(with subsequent loss of material to the filtrate). 

The second purpose is to avoid collapse of the 

filtration apparatus itself (i.e., filters, flasks, 

tubing, etc.). For CHLS, a 47-mm diameter filter 

(type A/E) is used and the maximum practical 

volume is filtered (20-1,000 mL commonly).

 The filtration apparatus is assembled with the 

47-mm glass fiber filter (type A/E) positioned 

with wrinkled side up. Suction is started and the 

filter is wetted with a small volume of reagentgrade water to seat it. In preparation for filtering, 

the sample is agitated in its container vigorously 

to resuspend any material that may have settled. 

The graduated cylinder used to measure the 

sample volume is rinsed first with a small volume 

of sample water before the measurement. After 

rinsing the cylinder, the capped water sample 

is agitated vigorously once more and a suitable 

volume (20–1,000 mL commonly) of sample is 

immediately poured into the graduated cylinder 

(type TD). See below for guidelines on highly 

concentrated samples. The measured volume is 

then poured from the graduated cylinder onto 

the seated filter and suction is continued for at 

least 30 sec after liquid has passed through the 

filter to ensure that the filter is damp dry. The 

funnel walls are then rinsed with three successive 

small volumes of reagent-grade water to move 

any particles clinging to the walls. The filtered 

sample volume (excluding the reagent water 

used for rinsing) is recorded. The damp filter is 

carefully removed from the apparatus, folded 

in half with the filtered material inside, and 

transferred to a labeled and bar coded storage 

planchet. The planchet and filter are wrapped in 

aluminum foil and stored frozen in darkness until 

ready for shipment to the LTRMP laboratory

 Several trade-offs must be made in this 

procedure. To maximize analytical accuracy, it 

is important to filter the maximum practicable 

volume. Once the filter has become clogged 

with material, the filtration rate drops abruptly 

and the time required to complete the filtration 

becomes impractical. When dealing with small 

filtration volumes (i.e., 50–100 mL) having high 

concentrations of suspended solids, a precision 

(±1%) pipette (i.e., 25–50 mL) should be used 

to measure out the sample volume instead of a 

graduated cylinder. Care must be taken to ensure 

the sample is vigorously agitated immediately 

before drawing off the sample and that the 

sample is taken from middepth in the container. 

Adding repeated small volumes of sample (i.e., 

20-mL increments) to the filter is generally 

unacceptable because measurement errors 

accumulate with each increment added (this is 

particularly true with graduated cylinders) and 

settling of material in the sample is increasingly 

likely. When repeated volumes must be used, 

precise and accurate (±1%) measuring equipment 

is essential and the number of incremental 

additions should be kept to four or less. Further, 

the sample container MUST be agitated 

vigorously before each subsample is withdrawn. 

If a graduated cylinder is used to deliver a 

single increment of sample and filtration time is 

prolonged (several minutes), then special care 
45

must be taken to ensure that all material is kept in 

suspension.

 Large particles (>2 mm) are not included 

in chlorophyll measurements made by the 

LTRMP water quality teams. This practice may 

exclude some large algal colonies, but these 

large colonial aggregates are not uniformly 

distributed in the water column at the scale 

of LTRMP measurements, they do not arrive 

at the laboratory intact (easily damaged 

by shipping and handling), and they create 

aberrant, nonreproducible results. The LTRMP 

near-surface samples (0.2 m) are specifically 

intended to exclude material floating on the 

water surface and field teams can avoid many 

of these large particulates (e.g., duckweed and 

vegetation fragments) by proper sampling. 

Several methods can also be used to remove large 

pieces of vegetation and other debris from the 

whole water sample before measurement and 

filtration for CHLS. Passing the water through 

a #10 sieve (2 mm, 0.0787 inch, USA standard 

testing sieve) or equivalent is appropriate. 

Large pieces of vegetation and other debris can 

also be individually plucked from the sample 

container using clean forceps or other suitable 

and clean device, but in most instances another 

sample should be collected. The surface of the 

filter media should be visually examined when 

filtration is complete. If large particulate is 

present, the filter must be discarded. It is not 

acceptable to manually remove particulate from 

the filter surface or from the filtration volume 

after it has been measured. If not enough sample 

volume remains to repeat the filtration and a 

replacement sample cannot be obtained (i.e., 

filtration is conducted in the laboratory), then 

the sample is lost and should be appropriately 

flagged (QF code of “5”).

6.1.2.2 Method—Fluorometric Chlorophyll-a 

Filtration 

 For CHLF, a volume of 5.00 mL is filtered 

through a 25-mm diameter filter (type A/E). A 

fixed-volume precision pipet is used for sample 

withdrawal and delivery. The same procedures 

described for CHLS (Section 6.1.2.1) are used 

for sample agitation and vacuum levels, as are the 

following additional instructions:

 a. The 25-mm glass fiber filters used 

for fluorometric chlorophyll-a are not 

prerinsed, but a few drops of DI water may 

be used to help seat the filter.

 b. You must filter exactly 5.00 mL of 

sample for fluorometric chlorophylla. In instances where large particles 

may be present, a widemouth pipette 

tip may be appropriate. Do not include 

any macroscopic vegetation or other 

large particulate (i.e., >2 mm) in the 

chlorophyll-a determination. Be sure to 

follow the exact procedures provided 

by the pipette manufacturer. For most 

models, the plunger is depressed to the 

first position while the pipette tip is in the 

air (not submerged in the sample). The 

plunger is released slowly and steadily 

after the tip is submerged in the sample. 

The 5.00 mL is delivered by depressing 

the plunger to the second position (some 

models require a blow out or wick step 

to eject the last portion of sample). Read 

the instructions carefully! Pipette tips are 

rinsed between samples. The pipette unit 

(not the individual tips) must be calibrated 

at the LTRMP laboratory or other 

analytical facility to ensure accuracy and 

precision of delivery.

 c. After the 5 mL has passed through the 

filter, the filter and funnel are rinsed with 

three successive portions of DI water (5–

10 mL) to ensure that all of the sample has 

been flushed onto the glass-fiber filter and 

to ensure that any dissolved fluorescent 

material is rinsed away. The damp filter 

is then carefully removed with forceps, 

folded sample-side in, and inserted into a 

culture tube.

 d. Culture tubes are not capped for storage 

or shipment. Once the filter is inserted 

deep into the tube and the bar code label 

is applied, tubes can be carefully and 

securely wrapped in at least two layers of 

aluminum foil (in groups of 5 to 10) to 

exclude all light. The tubes are then ready 
46 

to ship to the LTRMP analytical laboratory 

(keep frozen in darkness until shipment).

 

6.2 Phytoplankton

 Phytoplankton (drifting algae) are 

microscopic and near-microscopic plants that 

are the major source of primary production in 

lentic systems and are significant contributors 

to the food chain in large river systems, such as 

the Upper Mississippi River. The plankton of 

rivers are sometimes called potamoplankton. 

In ecological studies, phytoplankton have been 

collected with plankton nets in a manner similar 

to that still used for zooplankton. However, it 

has been found that a large portion of the active 

phytoplankton assemblage could pass through 

even the finest mesh nets. Phytoplankton samples 

are easy to collect and preserve, but processing 

of these samples is extremely time-consuming. 

The LTRMP approach is to collect and preserve 

whole-water phytoplankton samples routinely, 

but with the intention of processing only those 

samples that are later shown to be significant (as 

determined by other analyses or notable events). 

As of September 2003, none of the preserved 

phytoplankton samples in the LTRMP have been 

subjected to microscopic analyses.

6.2.1 Definition

 The LTRMP considers all microscopic and 

near-microscopic algae and cyanobacteria 

suspended in the water column to be 

phytoplankton.

6.2.2 Sample Collection and Preservation

 A suitable depth-discrete (Sections 7.3 and 

7.4) sample is collected. A whole (unfiltered) 

sample is preserved with Lugol’s iodine 

(Section 7.8.1). Enough preservative is added to 

give the sample a weak brown color (i.e., 0.2 mL 

per 60-mL sample)

6.3 Zooplankton

 Zooplankton (drifting animals) are 

microscopic and near-microscopic animals that 

can be a major source of nutrition for many 

young and larval fish, as well as filter-feeding fish 

and invertebrates. This group of organisms can 

exert major grazing pressure on phytoplankton 

and can also provide nutritional links among 

microorganisms, organic detritus, primary 

producers, and higher consumers. Zooplankton 

sampling is not difficult, but processing of 

zooplankton samples can be extremely timeconsuming and expensive. Consequently, the 

LTRMP has not routinely sampled zooplankton 

except in Lake Pepin, where separate funding has 

been provided to the Minnesota Department of 

Natural Resources to collect these samples.

6.3.1 Definition

 In the LTRMP, all drifting copepods, 

cladocerans, and rotifers suspended in the water 

column and trapped by an 80-micron mesh 

plankton net are considered to be zooplankton. 

This operational definition allows some 

organisms (i.e., rotifers smaller than 80 microns) 

to escape detection.

6.3.2 Sample Collection and Preservation

 The LTRMP zooplankton samples are 

collected by semiquantitative vertical tows using 

an 80-micron mesh plankton net. Before April 

1996, samples were preserved with buffered 

sugar-formalin and subsequently have been 

preserved with 80% ethanol that is diluted by 

the sample volume to a final concentration of 

40-50%.

7. Field Sampling of Physical 

and Chemical Water Characteristics

 This section describes the general procedures 

used to collect water samples and make in situ
47

measurements of selected physical and chemical 

properties of water. For details on the overall 

sampling design and the scheduling of field 

sampling, see Section 1. Important amplifying 

information required for the measurement or 

handling of specific chemical or biological 

constituents is provided in Sections 5 and 

6. Details on the recording of field data are 

presented in Section 8.

 In general, water samples collected for 

chemical analyses receive only that level of 

field manipulation needed to successfully 

transfer them back to the field station for 

further processing or shipment to the analytical 

laboratory. In situ measurements of chemical 

and physical properties are taken in a manner 

that ensures that these measurements accurately 

represent ambient conditions in the water column 

at the location (horizontal and vertical) and time 

of sampling.

 Measurements of in situ chemical and 

physical properties and the collection of samples 

for analysis are done near the water surface 

(0.2 m) at all sampling locations. Other depths 

are sampled as required (see Sections 7.3 and 

7.4). For in situ measurements, care is taken to 

ensure that the sensors themselves are located at 

the assigned sampling depth. Grab samples taken 

for analysis are collected so that the vertical 

midpoint of the collected water is at the assigned 

depth.

7.1 Sampling Site Inaccessible or Unusable

 River conditions, weather, and equipment 

failures occasionally make it impossible or 

unsafe to collect samples or measurements at 

a designated sampling location. Sections 1.6 

and 1.8 describe the use of alternate sampling 

locations in SRS, but in FSS there are no 

alternate sampling locations. To document 

conditions that cause a sampling site to be missed 

during a scheduled FSS sampling week or SRS 

sampling episode, a data sheet (Section 8.3) that 

includes the date, crew leader code, recorder 

code, and site comment is completed for the 

missed location. The site comment briefly 

explains the situation that caused sampling to 

be incomplete. The number of sample rows 

(NROWS; Section 8.3) on the data sheet is set 

to zero and no data or QF codes are entered in 

the depth rows. The time of sampling need not 

be recorded for a site that cannot be accessed. 

However, if a sampling time is recorded in this 

situation, it should be the time of arrival in 

the vicinity of the site. Note: Sampling times 

from data sheets with no detail rows completed 

(NROWS=0; Section 8.3) are excluded from 

computation of mean daily sampling times and 

other performance measures.

7.2 Shallow Water Sampling

 Sampling in shallow water (<0.5 m) presents 

special problems because of equipment size 

limitations and the possibility of sample 

contamination with bottom material. Generally, 

LTRMP routine monitoring does not attempt 

to collect grab samples in water <0.2 m deep. 

The only exception is in hard-bottom, flowingwater situations (e.g., concrete weir, gravel bed, 

or other hard surface in a flowing tributary) 

where a sample can be readily obtained without 

contamination with bottom material. Sampling 

in shallow water requires special attention to 

the actual vertical position of the in situ sensors. 

The difference between the bottom of the sensor 

guard and the probes is a significant fraction of 

the total sampling depth in this situation. If, for 

example, the sensor guard is in contact with the 

bottom, then the instrument may not be vertical 

and the in situ probes may be displaced from 

their expected depth in the water column.

 When approaching a shallow water site, 

special care must be taken to avoid disturbing 

the substrate. Whether using an air boat or 

conventional propulsion, the motor should be 

shut off or disengaged several meters from the 

sampling location and the boat allowed to drift 

into sampling position. Anchoring is required 

to obtain velocity measurements, but extreme 

care must be taken to avoid disturbance of the 

bottom. One approach to shallow-water sampling 

is to collect the water sample immediately after 

the boat drifts into position and before setting 

the anchor. This is, however, a compromise 

because it is desirable to take in situ readings 

(e.g., temperature, DO, etc.) at nearly the same 
48 

time as the water is collected. Any material that 

is resuspended or disturbed during approach to 

the site should be allowed to settle or drift clear 

before sampling commences.

7.3 Discrete-Depth Sampling

 In water deeper than 0.5 m, when only a 

surface (0.2-m) grab sample is needed, a plastic 

sampling bucket or a 2-L amber bottle may 

be used to obtain the sample. However, for 

discrete-depth sampling, a horizontal Van Dorn 

sampler (Wetzel and Likens 1991; Lind 1979) 

is recommended for collecting grab samples 

in moving or shallow (<0.5 m) water. This 

device is well suited for this application because 

of the narrow layer of water that it samples. 

However, the horizontal Van Dorn sampler is 

not recommended for discrete-depth sampling 

of subsurface water in deep (>1.9 m), stratified, 

calm water. This is because the horizontal Van 

Dorn sampler fills with surface sample when 

it first enters the water and, unlike a vertical 

Van Dorn sampler, this surface water tends to 

be carried along in the sampler as it is lowered. 

In flowing water, the surface sample dragged 

along with the device is flushed out by horizontal 

water movement and the problem is eliminated. 

However, in calm water, the operator must 

move the device horizontally after it has arrived 

at the desired sampling depth to replace water 

from upper layers with water from the depth 

of interest. This horizontal motion may not be 

fully effective because (1) it can mix the layer 

of interest and produce a mixed-depth (rather 

than depth-discrete) sample and (2) the water 

entrapped in the device during lowering may not 

be fully purged. Consequently, a conventional 

(vertical) Van Dorn sampler or similar device 

is recommended for depth-discrete sampling in 

deep, calm water. 

7.4 Subsurface Sampling Requirements

 Water quality monitoring in the LTRMP 

is designed to detect patterns and changes in 

those limnological features that are most likely 

to influence river biota. Thus, the vertical 

distribution of limnological characteristics in the 

water column is monitored within the LTRMP, 

but only where the vertical dimension is clearly 

important and monitoring can be conducted with 

safety and efficiency. It is well known that steep 

gradients in suspended sediment (and associated 

constituents) are common immediately above 

the bed of the main channel(s) in the UMRS, 

but the biotic significance of these gradients has 

not been established and vertical sampling in 

the main channel requires special equipment, 

is extremely time-consuming, and can be lifethreatening. Limnological characteristics known 

to have major biotic significance (e.g., oxygen, 

water temperature, pH, dissolved constituents) 

generally do not exhibit pronounced vertical 

stratification in the main channel(s) of the 

UMRS except during low discharge. The 

LTRMP data demonstrate that surface sampling 

provides a good indicator of these limnological 

characteristics when flow velocities exceed about 

0.1 m/sec. Thus, routine subsurface sampling 

of water quality in swiftly moving (0.1 m/sec) 

water is not performed in the LTRMP.

 Appendix H summarizes the following 

information and provides a useful key for 

assessing the need for subsurface sampling under 

LTRMP guidelines.

 Surface measurements (0.2 m below the 

surface) are collected at all water quality sites. In 

areas where current velocity is <0.1 m/sec (which 

may at times include the main channel) and 

available water depth (AWD) is at least 0.60 m, 

bottom measurements of temperature, dissolved 

oxygen, pH, and conductivity are required to 

be recorded. If stratification is documented (see 

below and Appendix H for details), then bottomgrab samples for additional constituents may be 

required at fixed sites only. Measurement and 

recording of in situ parameters at additional 

depths (i.e., profiling) is optional; however, 

chemical analyses of profile samples are not 

routinely performed.

 In FSS only, subsurface water samples are 

collected in low-velocity areas for chemical 

analysis (e.g., turbidity, suspended solids, plant 

nutrients) when water depth exceeds 1.9 m, and 

differences between surface and bottom of the 

water column meet any of the following criteria:
49

 1. Temperature difference >1.9°C

 2. Oxygen difference >3.9 mg/L

 3. Specific conductance differs from surface 

reading by more than 50%.

 Historically, bottom-grab samples 

were required during SRS; however, those 

requirements were dropped in 1998 because 

stratification was infrequent and the cost of extra 

field and analytical effort required was large for 

the additional information gained.

7.5 Sampling During Ice Cover

7.5.1 Suitability for SRS Sampling 

 The field team leader must always judge 

whether the sampling point is suitable for 

measurement. This decision is not based on the 

“representative” character of the site relative to 

its designated stratum, but only on the ability to 

obtain a valid sample of the location. When ice 

is not present, sites <0.2 m deep are recorded, 

but are generally not sampled. Likewise, when 

ice is present, a site that would have <0.2 m 

of water if it were ice free is not sampled, but 

general site (header) information is recorded. 

If a representative site would have >0.2 m of 

water when ice free, but is frozen to the substrate 

(Section 7.5.3) then no additional or alternate site 

is used because to do so would bias the sampling 

(sites frozen to the substrate would tend to be 

overrepresented). 

7.5.2 Sampling Requirements with Ice Cover

 When a hole is cut through the ice for 

sampling, the water that enters the sampling hole 

from below the ice should be relatively clear 

with no indication of disturbed substrate. Care 

must be exercised when there is little clearance 

between the ice and substrate to ensure that the 

bottom is not disturbed while boring the access 

hole. In shallow water areas (e.g., <1 m), it 

is highly recommended to stop the ice auger 

before it completely penetrates the ice and 

chisel the remaining few centimeters with an 

ice spud. The plunge and rotation of the auger 

blades upon penetration through the ice may 

cause undesirable sediment and water column 

disturbance. If this cannot be accomplished, then 

see guidance in Section 7.5.3. Depth definitions 

are complex when ice is present, and a diagram 

of sampling depths and definitions used in this 

situation may be helpful (Section 3.1, Figure 2). 

When sampling through the ice, the reported 

sampling depth (Z) for the near-surface sample 

is the vertical distance between the bottom of the 

ice and the point of sampling (recorded to the 

nearest 0.01 m). Thus, in all instances, the actual 

depth of a near-surface sample below the level 

of the free-water surface is the recorded depth 

(Z) plus the vertical extent of submerged ice 

(Zsice). Samples and measurements are normally 

collected 0.2 m below the bottom of the ice 

(if possible) and the depth of the sample (Z) is 

reported as 0.2 m. However, if water depth and 

ice thickness are such that measurements and 

samples can only be collected between zero 

and 0.2 m below the ice, then water samples 

for chemical analysis are not required and 

should never be taken if any possibility of 

substrate disturbance exists. However, in situ

measurements are required, and the appropriate 

value for Z (sample depth beneath the ice to the 

nearest 0.01 m) is recorded. If measurements or 

samples cannot be collected beneath the ice, then 

Z is reported as zero. In some instances (e.g., 

shallow, flowing water), it may be possible to 

obtain in situ readings in the hole; Z is reported 

as zero, but water samples are not required. Nearbottom measurements are not required unless 

there is at least 0.6 m between the bottom of the 

ice and the substrate (Section 7.4).

 The sampling and reporting of nonsurface 

sampling depths when ice is present is unchanged 

from ice-free procedures (Section 7.4) and is 

referenced to the free-water surface, not the 

bottom of the ice. For example, if the substrate 

is 70 cm below the bottom of the ice and Zsice

is 25 cm, then the substrate is 95 cm below the 

free-water surface. A surface sample is collected 

at 0.2 m below the bottom of the ice (Z = 0.20) 

and bottom measurements and samples (as 

appropriate) are taken 0.2 m above the substrate 

(Z = 0.95 – 0.20 = 0.75). All measurements 

except the near-surface are referenced to the freewater surface. Additional information on depth 
50 

definitions and snow and ice cover is found in 

Sections 3.2 and 3.8.

7.5.3 Ice Extends to Substrate

 When ice extends into the substrate, or the 

bottom of the ice is in such close proximity 

to the substrate that a sediment and water 

mixture (slurry) is forced into the access 

hole when the ice is penetrated, then the site 

is considered frozen to the bottom. In this 

instance, the guidance in Section 7.5.1 applies 

to SRS sampling and an appropriate comment 

is recorded on the data sheet. Further, Zmax at 

the site is reported as zero so that AWD can 

be correctly calculated as zero in the database. 

Note that submerged ice thickness (Zsice) is also 

reported as zero under these conditions and that 

Zmax and Zsice both receive QF codes of 5 (sample 

unusable or unobtainable). This approach 

ensures that the condition of the site is properly 

documented. 

7.5.4 Unconsolidated Ice 

 If ice is present but does not form a 

continuous cover over the water surface at the 

sampling location, then sampling depths are 

the same as in open water. However, if open 

water sampling depths are used, then recorded 

ice information must indicate ice depths (Zice) 

and (Zsice) of zero. This is necessary to properly 

interpret the recorded sampling depth (Z).

7.5.5 Ice Surface Submerged 

 The surface of the ice is sometimes below the 

surface of the water because of rain, snow melt, 

or subsidence under the weight of the sampling 

team and equipment. Several alternatives are 

available for sampling in this situation: (1) move 

as much equipment and personnel as possible 

away from the sampling site, (2) construct a 

low dike of snow or ice around the sampling 

site to prevent over-ice water from entering 

the sampling hole, and (3) look for a slightly 

elevated spot on the ice within the sampling 

radius. If none of these options are suitable, then 

the effect of the overlying water can be gaged by 

comparing the conductivity in the sampling hole 

to both the overlying water and to water directly 

beneath the ice. Carefully examining the water 

in the sampling hole for signs of gravity flow or 

convective movements can also be helpful. If the 

conductivity in the sampling hole is not within 

5% of the underlying water or other indications 

of contamination by over-ice water are present, 

then the site is considered inaccessible and an 

appropriate comment entered on the data sheet. 

However, if some data are desired from this 

situation, then all the measurements should be 

flagged as nonrepresentative (QF code of “6”) 

and an appropriate comment entered on the data 

sheet.

7.6 Chemical Sampling when Dissolved Oxygen 

is Less Than 1 mg/L

 Oxygen concentrations <1.0 mg/L are not 

frequently encountered in routine LTRMP 

sampling. However, these conditions do occur 

in the UMRS, particularly under ice cover in the 

northern reaches, in the vicinity of groundwater 

inflow, in dense beds of submersed aquatic 

vegetation, and in deep, stagnant, areas with 

high sediment oxygen demand. Chemical 

sampling from water that has a low-oxygen 

concentration requires special considerations 

because the chemical form and solubility 

of many constituents in low-oxygen water 

(particularly iron and manganese) are altered 

dramatically when exposed to air. For example, 

field teams have seen clear samples become 

cloudy with precipitate after being filtered or 

transferred to the sample bottle. As a result of 

this precipitation, the concentration of dissolved 

iron and manganese and co-precipitated materials 

(e.g., phosphorus) in the sample returned to 

the laboratory do not represent conditions in 

the river. The LTRMP has not targeted lowoxygen waters for specific study, and so the 

extra measures needed to accurately sample a 

wide range of chemical constituents under such 

conditions have not been included in routine 

monitoring. It is important, however, that these 

conditions be appropriately documented so that 
51

the laboratory is prepared for the condition of the 

samples and to ensure that the resulting analytical 

results can be interpreted correctly. This is 

accomplished by recording appropriate site and 

sample comments on the data sheet (Section 

8.3). The lab software (ScanLog32) alerts lab 

personnel when individual sample comments are 

recorded.

7.7 Selecting Sites for Chlorophyll-a Calibration 

and QA/QC

 To calibrate CHLF, samples are collected 

for CHLS at approximately 10% of the CHLF 

sampling sites. Phytoplankton samples are also 

collected at these locations. The selection of 

calibration sites is randomized to avoid bias and 

because more CHLS sites than QA/QC sites are 

required (10% vs. 5%), a subset of the CHLS 

sites should be used for QA/QC. In SRS, the 

number of CHLS sites in each sampling stratum 

is proportional (10%, rounded up to the nearest 

whole number) to the total number of sites 

sampled in the stratum.

7.7.1 Method

 First, the required CHLS sites for each 

stratum are picked randomly from the list of 

full chemistry sites. For example in Pool 4, 

the 10% requirement specifies the following 

allocation: main channel = 3, side channel= 3, 

Lake Pepin = 3, and backwater = 5 (see Table 3). 

Randomization can be done by assigning a 

random number to each full chemical site in the 

sampling episode and then sorting the list of 

sites in descending order by stratum and random 

number. After sorting, the top sites from the list 

within each stratum are picked until the required 

number for each stratum is obtained. A simple 

SAS program can perform these operations 

(Appendix I). All the sites selected in this step 

are used as CHLS sites. Of these sites, one per 

day per work block is also used as a QA/QC site. 

If none of the selected sites occur in the daily 

work block, then an additional site for that block 

is picked randomly. If multiple CHLS sites are 

located in the daily work block, then the site with 

the highest randomly assigned number is used for 

the QA/QC site.

 The number of QA/QC sites required during 

the episode will generally equal the number of 

team days required to complete the episode. For 

example, seven QA/QC sites are required for 

a 7-day, 140-site SRS episode with one team 

in the field on each day. However, if sampling 

is completed in 4 days with two teams in the 

field each day, then eight QA/QC sites will be 

required. If an additional QA/QC site is needed 

beyond those originally scheduled, then the 

highest random number in the CHLS site list 

within the daily work block is used for the 

additional QA/QC site.

 Blocks of sites are picked that can be sampled 

in 1 day by a single team. The 6 to 10 daily 

blocks are then randomly assigned to teams 

and to workdays. If a large area (e.g., Lake 

Pepin) is to be sampled on two consecutive 

days, then one of the blocks in the sequence is 

selected randomly and randomly assigned to a 

workday (Friday would be excluded from the 

random choice of days). The second block in the 

sequence is then sampled on the following day.

7.8 Sample Preparation For Shipment and Analysis

 Some processing of samples is normally 

conducted after samples are returned to the 

field station and only three containers need be 

collected in the field at each sampling site and 

depth. Two of these (60–125 mL) will contain 

water that is filtered and acid-preserved on-site 

(Section 7.8.1), the third (2 L) is unfiltered and 

unpreserved and may be processed in the field 

or returned to the field station laboratory for 

additional processing. The 2-L sample must be 

held on ice and in the dark until processing is 

completed (within 24 hours of collection). The 

unfiltered sample can be used for determination 

of specific conductance, turbidity, suspended 

solids, chlorophyll-a, phytoplankton, total 

nitrogen, and total phosphorus.

 It is recommended that all the smaller (i.e., 

60-mL) sample containers from a single location 

and depth be placed into a single zipper-lock 

bag or other suitable container to keep them 
52 

organized. An additional label written in pencil 

or waterproof ink should be placed inside the bag 

to identify the sampling location and depth.

7.8.1 Sample Treatments

 Before water samples are brought back 

from the field or shipped to the analytical 

laboratory, they receive one of the treatments 

listed (Figure 3) to prepare them for shipment or 

analysis. Note: hydrochloric acid preservation 

is not used presently in LTRMP but is listed for 

reference. All the constituents associated with 

a treatment are not necessarily analyzed in the 

LTRMP: 

 a. Unfiltered, No Preservative Added.

Suitable for turbidity measurement in the 

laboratory or subsequent processing for 

total suspended solids, volatile suspended 

solids, and chlorophyll-a measurement 

(Sections 4.5 and 6.1).

 b. Unfiltered, Preserved with Sulfuric Acid 

(pH 2.5–3.0). Suitable for total nitrogen, 

total Kjeldahl nitrogen, total phosphorus, 

total iron and manganese, and total organic 

carbon. Although this sample is unfiltered, 

care must be taken to ensure that large 

(>2-mm) particulates (e.g., leaves or other 

pieces of vegetation, insects, larval fish) 

are excluded. This is necessary because 

the analytical laboratory cannot prepare 

a homogeneous sample for multiple 

determinations if large particulate material 

is included.

 c. Unfiltered, Preserved with Lugol’s Iodine.

Used for phytoplankton samples, Lugol’s 

iodine is added in sufficient quantity to 

impart a tealike color to the sample.

 d. Filtered, Nonpreserved. Suitable for color, 

SRP, alkalinity, chloride, sulfate, and silica 

determinations.

 e. Filtered, Preserved with Sulfuric Acid 

(pH 2.5–3.0). Suitable for nitrate plus 

nitrite nitrogen, ammonia nitrogen, total 

dissolved phosphorus, acidified soluble 

reactive phosphorus (SRPH), total 

dissolved Kjeldahl nitrogen, and total 

dissolved organic carbon.

 f. Filtered, Preserved with Nitric Acid 

(pH 2.5–3.0). Suitable for dissolved metal 

cations.

Figure 3. Treatments used to prepare samples for shipment to the Long Term Resource Monitoring Program analytical 

laboratory.
53

 g. Filtered, Preserved with Hydrochloric Acid 

(pH 2.5–3.0). Not used in the LTRMP, but 

suitable for some dissolved metals cations 

(Ca, Mg, Na, K) and dissolved organic 

carbon.

 In addition to water samples, filtered residue 

is shipped to the analytical laboratory for further 

chlorophyll-a and suspended solids processing 

(Sections 4.5 and 6.1).

7.8.2 Filtration of Inorganic Chemical Samples

 Two-stage filtration is used routinely in 

the LTRMP to prepare chemical samples for 

shipment and analysis of inorganic dissolved 

species (i.e., metals, nitrate, nitrite, ammonia, 

chloride, silica, SRP). Filtration for these 

constituents is normally completed on-site within 

20 min of sample collection, or appropriate 

comments and QF codes are entered on the data 

sheet (Sections 8.3 and 8.4). To avoid crosscontamination, new filtration media are used 

for each sample. The first-stage filtration uses a 

glass-fiber (type A/E) filter, followed by a second 

(final) filtration through a 0.45-μm, surfactantfree, cellulose acetate membrane filter (Nalgene® 

191-2045). These steps are usually performed 

in a combined two-stage filter, but where 

necessary, the filtrate from suspended solids or 

chlorophyll-a filtration can be used as the first 

stage, followed by processing through a 0.45-

μm membrane. It is essential that the filtration 

apparatus and filtrate container be rinsed at least 

twice with a small volume (5–20 mL) of sample 

filtrate before water is kept for analysis. The 

initial flush of sample (5–20 mL) through the 

filter apparatus serves to remove carryover on 

the apparatus walls from the previous sample 

and removes most contamination that may be 

leached from the filter itself during subsequent 

filtration. If constituents from the sample adsorb 

to the filter media, this initial flush is intended 

to saturate or equilibrate the adsorption process. 

The flush water is discarded. The syringe 

filters in use by the LTRMP (Nalgene® 25-mm 

Syringe Filters Cat. 191-2045) have a maximum 

operating pressure of 75 psig/5.1 bar, which can 

be exceeded with the use of mechanical pressure. 

Extreme care must be taken to ensure that the 

maximum operating pressure is not exceeded. 

Filtration equipment must be checked with an inline pressure gage periodically and before initial 

use to ensure that maximum pressures are not 

exceeded.

 Although two or more differing containers of 

filtered water (acidified, not acidified, QA/QC 

split, and QA/QC split plus spike) may be sent 

to the laboratory for each sample, the filtered 

water used to fill all these containers must 

come from a single common “pool” of filtrate. 

Therefore, enough water must be filtered into a 

common container to supply all the acidified and 

unacidified sample bottles for the original sample 

and the QA/QC (as appropriate). The common 

filtered sample may be held in any sample 

container with adequate capacity that also meets 

the requirements of cleanliness and material 

composition for the analytes being sampled. 

 For samples and analyses in which the 

phytoplankton cell contents are of little or no 

quantitative consequence (i.e., total suspended 

solids with high inorganic content), vacuums, or 

pressures are limited only by the limitations of 

the filters and filtering apparatus.

7.8.3 Acid Preservation of Samples

 Standard Methods (APHA 1992) for the 

acid preservation of samples calls generally 

for pH levels <2.0, but extremely low pH has 

been found to interfere with automated sample 

analysis (i.e., because of altered reaction rates 

and color development) at the LTRMP analytical 

laboratory. Therefore, for acid preservation of 

samples in LTRMP water quality monitoring, 

a pH level between 2.5 and 3.0 is specified. 

Field teams verify that this level is attained by 

use of pH test strips in the field. Preservation 

is performed with reagent grade acid that is 

certified to contain no LTRMP analytes at 

concentrations >1 ppb. Care must be taken 

to ensure that the acid and acid-dispensing 

equipment does not become contaminated. The 

dispensing container must remained sealed and 

kept inside a protective outer container (e.g., 

plastic bag) when not in use. Immediately before 

acid is added to the first sample at a new location 

(or more than 30 min have elapsed since acid 
54 

was dispensed), a few drops of acid should 

be dispensed into a proper waste container to 

clear any contaminant from the dispenser. The 

dispensing device must be handled in such a way 

that contaminated or used acid is not drawn back 

into the dispenser. Disposable, powderless gloves 

are worn when handling acid.

 Acid preservation should be performed only 

in the field after sample water has been placed 

in the sample container (add acid to water, 

not water to acid). Sample containers should 

not be “preacidified” with concentrated acid 

before proceeding into the field. Although this 

practice is attractive because it allows all acid 

handling to be conducted in controlled conditions 

and removes the need to transport significant 

volumes of dangerous chemicals into the 

field, it creates problems. Specifically, holding 

concentrated nitric and sulfuric acid in plastic 

sample containers degrades the plastic, creating a 

range of breakdown products, and can make the 

container brittle. It can also impregnate the walls 

of the sample container with analytes (nitrate, 

sulfate, etc.) that are not removed by normal 

washing, but leach slowly into samples during 

storage.

 Acid preservation of filtered samples is 

performed as follows:

 a. Partly Fill the Sample Bottle to be 

Acidified. The sample to be acidified 

is processed before the nonacidified 

sample so that if something goes wrong 

(i.e., excess acid is added), the acidified 

sample can be discarded and additional 

water can be filtered into the common, 

unpreserved, filtrate pool (Section 7.8.2) 

for a second try. If the nonacidified sample 

were processed first and then a mistake 

was later made in processing the acidified 

sample, then the entire volume of both 

the nonacidified and acidified sample 

would have to be discarded because 

(1) any additional filtrate required to 

prepare the acidified sample would not 

come from the common filtrate pool used 

to fill the nonacidified sample container 

and (2) water cannot be transferred 

back into the common filtrate pool from 

the unacidified container because of 

contamination risk.

 b. Adjust the pH. The goal is to add the 

minimum amount of acid required to 

get the sample into the proper pH range 

(2.5–3.0). Keep in mind that one drop 

(0.03 mL) of concentrated acid in 60 mL 

of distilled water will produce a pH of 

about 1.7. Therefore, depending on the 

buffering capacity of the sample, one drop 

of acid may be enough. Also, keep in mind 

that below pH 4.5 the buffering capacity of 

most water drops off dramatically (because 

bicarbonate has all been converted to 

carbon dioxide). Test the pH with a 

fresh test strip as needed. Beware of the 

contamination potential. Test strips are not 

inserted into sample containers, but a few 

drops of preserved sample are dropped 

onto the test strip to determine pH. 

 Experience over the years has shown the 

approximate additions of acid (Table 10) that 

create the proper pH in 60-mL samples from the 

Upper Mississippi and Illinois Rivers.

 c. Add the Remaining Filtered Volume and 

Seal the Container. After the acid has been 

added, the remaining volume of filtered 

water can be added to the sample bottle. 

With 125-mL bottles, this sequence is not 

critical, but because 60-mL bottles are 

used by the LTRMP, it will be necessary 

to leave enough headspace so that acid 

can be added without splashing any acid 

or sample from the container. In QA/QC 

Table 10. Acid additions required to reach the desired pH for 

preservation of 60-mL Long Term Resource Monitoring Program 

water quality samples.

Acid

preservative Sample type

Volume

added

Concentrated 

sulfuric acid

Dissolved 

inorganic 

nitrogen

1B2 drops 

(30B60 μL)

Concentrated 

nitric acid

Dissolved metals 5B6 drops 

(150B180 μL)

Concentrated 

sulfuric acid

Total nitrogen 

and total 

phosphorus

1B3 drops 

(30B90 μL)
55

procedures, the sample bottle (volumetric 

flask) is filled to the volume mark with 

additional sample after the acid is added. 

This final topping off of the sample will 

raise the pH slightly (typically <0.1 pH 

unit).

 Acid preservation of unfiltered samples is 

performed as with filtered samples except that 

the order of sample processing is not critical 

because a single pool of filtered water is not 

used. Unfiltered water may have slightly greater 

buffering capacity than filtered water because 

of suspended carbonates and other buffering 

materials and may therefore require slightly 

greater acid addition to reach the desired pH.

7.8.4 Filling of Sample Bottles: Rinsing 

and Agitation

 Sample containers should be rinsed with 

sample twice before keeping the final sample. 

Adequate headspace must be left in the 

subsample container for preservatives and 

freezing. Containers should be filled to the 

rounded shoulder of the bottle (about 10 mL 

of empty space in a 60-mL bottle). Suspended 

particulate material in river water can settle 

rapidly; therefore, it is critical that whole-water 

samples be vigorously agitated before and during 

transfer to subcontainers (including transfer to 

filtering apparatus). In LTRMP water quality 

monitoring, pumps may be used for delivery 

of sample water to the filtration apparatus, but 

not for the transfer of whole water samples into 

subcontainers (Section 7.8.5).

 Care must also be taken to ensure that 

contaminants (including dust, rain, and snow) do 

not enter the whole water or subsample container 

during the transfer process.

7.8.5 Filtration Using a Peristaltic Pump

 Instead of using a syringe to pressure-filter 

a sample, a peristaltic pump may be used to 

transfer the water sample into the filtration 

apparatus under suitable low pressure. This 

is only applicable when the filtrate is to be 

analyzed; it is not appropriate when the 

particulate phase of the sample is to be retained 

(i.e., suspended solids or chlorophyll-a analysis). 

The preferred method for obtaining filtrate by 

pump-driven filtration is to place a subsample 

(split) from the collected ambient water sample 

into a separate container for filtering (e.g., plastic 

cylinder) that serves as the source water for the 

pump. The main sample must be appropriately 

agitated immediately before the subsample is 

transferred into its separate container where 

further mixing is performed. In some situations 

(e.g., ice forming in the sample and on the 

apparatus), it may not be feasible to transfer a 

subsample to a separate container for filtration. 

In this instance, the primary sample may be used 

as the source water for pump filtration (and used 

as a whole-water sample) if precautions are taken 

to ensure that the filtering procedure does not 

alter the composition of the primary sample by 

selectively withdrawing particles or supernatant: 

(1) any whole-water subsamples should be 

withdrawn before filtration commences; (2) the 

primary whole-water sample should be agitated 

during filtration at least once every 60 sec or 

whenever the filter media is changed, whichever 

comes first; and (3) the primary sample is fully 

remixed whenever sediment is observed on the 

container bottom or a gradient in particulate 

concentration is observed in the sample 

container.

 The following additional guidelines must be 

followed when filtering samples: (1) because 

the filters have pressure limits specified by the 

manufacturer and mechanical pumps can easily 

exceed those limits, it is imperative that pressures 

be checked periodically by a suitable means 

(e.g., in-line gage). Filter membrane rupture 

can occur without any visible signs of defect. 

(2) Mechanical devices intended to increase 

hand pressure by way of leverage (e.g., “cancrushers”) can produce pressures much greater 

than filter limits and are not easily controlled. 

Their use is therefore strongly discouraged. 

(3) Past experience has demonstrated quality 

control problems with some filter manufacturers; 

therefore, the only final-stage filter approved for 

LTRMP use is the Nalgene® 25-mm syringe 

filter (Cat. 191-2045).
56 

7.8.6 Freezing of Samples for Preservation 

 Chlorophyll-a, suspended solids, soluble 

reactive phosphorus, silica, and chloride samples 

may all be preserved by freezing at temperatures 

at or below -10°C. Chlorophyll-a samples must 

be kept in total darkness while frozen and any 

exposure to acid fumes during storage must 

be rigorously avoided. Do not store acid in the 

refrigerator used to hold samples and keep the 

freezer or refrigerator in an area that is isolated 

from any acid washing or other acid use.

7.9 Holding Times For Storage 

and Shipment of Chemical Samples

 Analysis of water samples for chemical 

constituents should be performed as soon as 

practicable to avoid changes in the sample during 

storage. Sample holding times and conditions are 

published in Standard Methods (APHA 1992, 

1998) and are observed by the LTRMP, with 

some exceptions (cf. Table 11). Note that total 

holding times are from sampling to analysis, 

not just the time held at the field station before 

shipment to the laboratory. Keep in mind 

that samples may be held 1 to 3 weeks in the 

laboratory before analysis.

7.10 Sample Containers: Size, Composition,

and Integrity

 All samples that are shipped to the laboratory 

for analysis must be placed in the appropriate 

size and type container (Table 11) and must be 

properly tagged to ensure correct storage and 

handling. All containers must be leak-free (with 

a tight seal) so that the sample does not leak out 

and contaminants are unable to enter. Leaking 

containers are sometimes difficult to detect when 

sample bottles are kept in an ice-water mixture, 

and this practice should be avoided. If a leak is 

detected in a sample bottle AFTER it has been 

immersed (i.e., in a cooler of ice-water), the 

sample must be discarded as contaminated—it 

cannot be transferred to another container.

Table 11. Preservatives, containers, and holding times used for water quality monitoring samples in the Long Term Resource 

Monitoring Program.

Constituent Preservative Container type and size Holding time

Chlorophyll-a Total darkness, 

freezing

Planchet, glass fiber 47 mm; 

culture tube, glass fiber 25 

mm

30 days dark, frozen

Dissolved metals HNO3, pH 2.5-3.0 Plastic (60 mL) 60 days

Dissolved Si, chloride, soluble 

reactive phosphorus, sulfate 

Freezing Plastic (60 mL) For SRP, 48 hours 

unfrozen, 28 days 

frozen. For silica, 

28 days (silica must 

be at pH >6)

Nitrate, nitrite, ammonium H2SO4, pH 2.5-3.0 Plastic (60 mL; glass 

container also acceptable)

28 days

Phytoplankton Lugol’s iodine Amber Indefinite after 

preservation

Suspended solidsa Freezing Planchet, glass fiber 47 mm 28 days after 

filtration, kept 

frozen

Total nitrogen and phosphorus H2SO4, pH 2.5-3.0 Plastic (60 mL) 28 days

Zooplankton Ethanol, 80% Not specified Indefinite after 

preservation

a

Holding time in Standard Methods (APHA 1992) is 7 to 14 days.
57

 Plastic containers can become brittle with 

age and after exposure to acid. This is often 

accompanied by discoloration of the plastic. Any 

containers that become discolored or inflexible 

should be discarded.

 Before shipment to the laboratory for 

analysis, field samples must be processed as 

described previously in this section and (if 

necessary) transferred to appropriate containers. 

The LTRMP follows the specifications of 

Standard Methods (APHA 1992) regarding 

the composition of containers used for holding 

samples for analyses (Table 11).

7.11 Quality of Water for Cleaning 

and Sample Preparation

 One of the most important aspects of chemical 

analysis is the preparation of reagent water used 

for dilution, washing, and preparation of blanks. 

Water used for cleaning of sample containers 

and sampling equipment or used in analysis and 

sample (blank) preparation in LTRMP is called 

deionized (DI) water and must meet published 

standards of purity (APHA 1998). This is gaged 

by the conductivity of water. Commercially 

available distilled water cannot be assumed to 

meet these standards without verification. If 

possible, reagent-grade water should be obtained 

from the LTRMP analytical laboratory or other 

quality controlled source. Water is prepared by 

the LTRMP laboratory using ion exchange and 

micro-filtration (0.45 μm) and typically has a 

resistivity of 17–18.2 megohm-cm at 25°C when 

fresh. Water used for blank preparation in the 

field should have a resistivity of >1-megohmcm (<1 μS conductivity) at 25°C. Low-quality 

water (APHA 1998) suitable for field washing 

of equipment should have a resistivity of 

>0.1-megohm-cm (<10 μS conductivity) at 25°C.

7.12 Cleaning of Sample Containers

 All containers used for sample collection, 

storage, or shipment must be appropriately 

cleaned. For the inorganic constituents analyzed 

in LTRMP, cleanliness can be verified by testing 

the conductivity of rinse water from cleaned 

containers. To conduct this test, a cleaned 

container is rinsed with a volume of reagentgrade water (specific conductance <0.5 μS or 

resistivity of >2-megohm-cm) not exceeding 40% 

of the total container volume (i.e., <25 mL of 

rinse for a 60-mL container). The resultant rinse 

water should have a specific conductance 1 μS 

(or resistivity of 1-megohm-cm at 25°C). 

Statistical-based quality control in which at least 

10% of all bottles washed are subjected to testing 

provides acceptable verification of cleanliness. 

In July 2001, the LTRMP implemented a central 

facility for machine washing of all sample 

containers used for chemical analysis. This 

facility exceeds the 1-μS standard for rinse water 

on clean bottles, and greater than 10% of all 

bottles washed are subjected to quality control 

tests. All batches of clean bottles are tested for 

compliance with the above cleanliness standards 

before release to the field teams.

 Manual washing of sample bottles used for 

shipment of inorganic chemical samples to the 

laboratory is no longer routine in the LTRMP, 

and the following guidance is provided for 

historical reference and for use in exceptional 

or emergency circumstances when laboratorywashed bottles cannot be obtained. Inorganic 

chemical samples shipped to the laboratory in 

hand-washed bottles after July 2001 should be 

marked with appropriate QF codes and data 

sheet comments. Except as noted below for 

chlorophyll-a and phytoplankton, all handwashed containers used for the analysis of 

chemical constituents are cleaned using (1) a 

soap-and-water wash with phosphate-free 

detergent, (2) tap water rinse, (3) acid soak, and 

(4) a final distilled water rinse as follows:

 a. Add a few milliliters of Liquinox® 

detergent (phosphorus-free; Alconox, NY) 

to a clean washtub or sink and fill with hot 

tap water. Thoroughly scrub the inside of 

exposed areas and the outside of glass and 

plasticware.

 b. Rinse off all traces of soap with hot tap 

water, then thoroughly rinse twice or until 

the glassware is free of all traces of soap. 

This is an important step.

 c. Using powder-free gloves, fully submerse 

the item in the acid bath (10% HCl) and 
58 

soak for at least 30 min but no longer than 

2 hours.

 d. Remove item and rinse immediately with 

reagent-grade water at least three times; 

do not set glass or plasticware on counter 

during this process.

 e. Set cleaned item on precleaned drying 

area with sample surfaces facing down to 

prevent dust contamination. Place small 

items (e.g., caps, glass stoppers, forceps) 

and fully exposed items in a tent of foil so 

dust will not contaminate surfaces and to 

allow to dry to completion (2–3 days).

 The following containers are subjected 

to cleaning processes that differ from those 

described above:

 a. Chlorophyll-a. Fluorimetric cuvettes are 

not cleaned before use. However, cuvettes 

with obvious soiling, chips, or scratches 

are discarded. It is essential that no 

containers used in any step of chlorophylla analysis (including sample collection) 

come in contact with acid or acid fumes. 

Note that hydrochloric, nitric, and acetic 

acids are volatile, and the fumes can 

permeate an entire room. Sulfuric acid is 

nonvolatile, but any trace of sulfuric acid 

solution left on a surface or in a container 

will concentrate as the water evaporates.

 b. Phytoplankton. Hot water (>40°C) 

followed by a single distilled water rinse is 

adequate for phytoplankton containers.

 c. Two-liter Container for Raw Water.

Hot water (>40°C) rinse with vigorous 

agitation. Pressure spray or brush is 

used as needed to remove any adhering 

material. No acid or detergent can be used 

for these containers. Following hot water 

rinse, the containers receive two rinses 

with reagent grade water.

7.13 Cleaning of Sampling Devices and Tubing 

 Because LTRMP water quality monitoring 

does not include trace substances (<1 μg/L) 

or organic contaminants, sampling equipment 

and tubing need not be subjected to cleaning 

by caustics, solvents, or detergents between 

sample sites. Repeated rinsing with ambient 

sample water before sample collection is usually 

sufficient. Tubing used for sample collection 

by pump is cleaned by allowing at least 5-tube 

volumes of sample water to pass through the 

tubing before sample collection. Care is taken to 

ensure that no particulate material has settled in 

the tubing. Grab-sampling devices, such as Van 

Dorn samplers, are cleaned by submergence at 

the sampling location. At the end of a sampling 

day, tubing should be cleaned with a rinse of 

10% HCL, followed by a thorough rinse (at least 

10-tube volumes) with reagent grade water. 

 Warning! Sampling devices (including tubing) 

can harbor invasive species (some microscopic) 

during transport among sites. Proper care must 

be taken to ensure that sampling equipment does 

not transport exotic species (e.g., zebra mussels) 

into pest-free areas. Flushing equipment with 

household bleach should suffice usually, but 

field teams should consult with local resource 

managers to ensure that specific threats are 

being properly addressed with this approach. 

Field crews must also take care that sanitation 

measures do not damage or contaminate their 

sampling equipment and should consult with the 

component coordinator in the development of 

specific sanitation procedures. 

7.14 Bar Code Labeling of Samples 

and Data Sheets

 A total revision of the LTRMP water quality 

data sheet was implemented in spring 1993. The 

new data sheet (Section 8, Figure 4; Appendix J) 

includes the use of bar codes for automated 

tracking of samples and data. Bar codes serve 

three major purposes in LTRMP water quality 

monitoring operations:

 a. Streamlined Error Tracking and 

Correcting. Every item of data in the 

database is permanently linked to the bar 

code on its original data sheet so that every 

item (or error) in the LTRMP database has 

a simple, unambiguous identity and can be 

tracked quickly and easily to its ultimate 

source.

 b. Streamlined Laboratory Handling and 

Tracking. The sample bar code is used 

to track samples through the analytical 
59

laboratory. The analytical results from 

the laboratory are linked back to the data 

sheets by these bar codes. This allows 

the laboratory to easily and efficiently 

track samples and analytical results. It 

also provides a method for conducting 

laboratory QA/QC blind testing.

 c. Data and Sample Accounting and 

Accountability. The bar codes provide 

an automated method for tracking 

data and samples through the entire 

processing system. Data or samples that 

are lost, duplicated, overdue, or otherwise 

mishandled will be readily detected and 

appropriate corrective action can be taken.

 The use of bar code labels in the LTRMP 

water quality monitoring has undergone revisions 

since 1993, but in general, the bar code labels are 

used as follows:

 a. Bar code labels are not taken into the field; 

they are attached to sheets and sample 

containers at the field station. A temporary 

labeling system is used in the field (colorcoded tags are provided for this purpose).

 b. Each data sheet receives a unique data 

sheet bar code label; this bar code is 

printed (or adhesive label attached) at the 

top of the data sheet in the space provided.

 c. Each sample collected also has an 

associated bar code. One copy of the 

sample bar code is attached (or printed) on 

the data sheet in the space provided and 

one is attached to each bottle, planchet, 

etc., associated with a sample. Bar code 

labels are attached to sample containers 

in such a manner that the entire bar code 

(1) is visible to the scanner (i.e., not 

wrapped around corners); (2) appears 

in a single plane (flat); and (3) does not 

interfere with analytical instruments 

(e.g., fluorometer cuvettes must be 

labeled outside the optical section of the 

cuvette). For samples with color-coded 

tags, the bar code is attached to the tag. 

Although the sample bar code is the only 

identifying information that the analytical 

laboratory records or uses for individual 

sample identification, samples that require 

supplemental information for processing 

(e.g., tare weight or filter volume) must 

be properly labeled with this additional 

information. Filter volumes are included 

in the electronic data sheet transmitted to 

the laboratory over the Internet. Future 

enhancements are planned for tare weights 

to be tracked by the laboratory with a 

separate bar code label. Additional details 

are provided in Section 8.6.

7.15 Sample Submission Procedures

 All samples for laboratory analyses are 

sent to the LTRMP laboratory at La Crosse, 

Wisconsin, by overnight courier and are preceded 

by electronic sample records transmitted to the 

laboratory over the Internet using file transfer 

protocol (FTP). A different transfer protocol 

(e.g., Virtual Private Network) will probably be 

implemented in 2004 to overcome the security 

issues associated with FTP. These records 

describe the number and type of samples 

included in the shipment, their identifying bar 

code numbers, and all other information recorded 

on the field data sheet. The electronic records 

(log files) are created by a field team member 

using computer software specifically developed 

at UMESC for this purpose (ScanLog32). An 

earlier version of this software (1994 to 2000) 

produced electronic files that were transmitted 

by field teams to the laboratory by electronic 

mail (e-mail). The version of the software now 

in use generates and transmits records directly to 

UMESC using the Internet and FTP. Additional 

details are provided in Section 8.6.

7.15.1 Scanning Samples for Custody Tracking 

and Shipment

 Field teams use the ScanLog32 software to 

scan and check the bar code on each sample as 

it is placed in the shipment container; this is to 

produce a verified custody record of all samples 

that were placed in the shipment container and 

sent to the laboratory. After this final scan is 

complete, the shipment container should be 

sealed and shipped. The ScanLog32 software 

will notify the user when all samples have been 
60 

accounted for, and it will then print paper copies 

of the data sheet for local archiving and also 

transmit the data sheet records to the LTRMP 

laboratory.

7.15.2 Packaging Samples for Shipment 

 The ScanLog32 software is tightly coupled 

to the concept of a sample batch (Section 8.1) 

and requires that samples and data be grouped in 

batches and that each batch be processed and sent 

to the laboratory as a single entity. This concept, 

however, does not preclude the field team from 

sending multiple batches to the laboratory in a 

single shipping container. This is an acceptable 

practice when multiple types of sampling (SRS, 

FSS, or special projects) have been conducted 

during the same interval (e.g., same week) and 

it is efficient to combine samples from multiple 

batches in a single shipping container (cooler). 

When samples are shipped this way, the batches 

must be kept separate and identifiable (i.e., in 

separate, labeled, zipper-lock bags) within the 

shipping container.

 Successful shipment to the laboratory requires 

that all samples remain cold during shipment 

and that frozen samples not thaw before arrival 

at the laboratory. It is also necessary to pack 

the shipment so that glass containers (e.g., 

fluorometric chlorophyll-a tubes) do not break, 

and planchets and chlorophyll-a tubes are not 

exposed to moisture that results from sample 

leakage or condensation. The external surface of 

sample containers should be dry before shipment 

to make leakage obvious and to minimize 

damage to bar code labels and other materials in 

the shipment. To further protect bar code labels 

on frozen samples, a paper towel or other suitable 

moisture-absorbing material should be placed 

inside sealed bags of sample bottles to trap 

condensation and any melt water derived from 

frost.

 To prevent thawing of frozen samples during 

shipment, the frozen samples should be packed 

toward the center of the cooler. Plastic containers 

of frozen coolant (commercially available 

or prepared using 2:1 ethylene glycol:water 

solution in clean plastic beverage containers 

with 10% headspace) should be packed around 

(and among) frozen samples. Planchets and 

chlorophyll-a tubes are placed in sealed 

bags above midheight in the cooler (to avoid 

immersion if leakage occurs). Some teams have 

used “bubble wrap” to encase the chlorophyll-a

tubes, but generally this is not required. The 

cooler should be filled with samples, coolant, and 

auxiliary packaging material as needed to prevent 

any significant free movement of the samples 

within the cooler during shipment.

 In completing the shipping label, be careful 

that all necessary fields, particularly the 

destination address, are complete and legible. 

Obtain and hold the documentation provided 

by the carrier until the shipment arrives at the 

LTRMP laboratory. The outside of all shipping 

containers should have the name, address, and 

phone number of the field station permanently 

marked and clearly visible on multiple surfaces. 

This may allow the shipment to be recovered 

if the shipping label is defaced or removed in 

transit. Standard overnight delivery is used 

routinely. Do not ship on Friday or immediately 

before a federal holiday as the LTRMP laboratory 

will not be able to receive the samples on the 

following day.

8. Field Data Recording and Reporting

 Water quality data sheets provide the basic 

information collected by LTRMP water quality 

monitoring. The data sheet is used to record 

conditions and samples collected (custody) at 

each monitoring site and to document sites that 

are inaccessible or not sampled for a variety of 

reasons. Because the water quality data sheet, 

in either paper (Appendix J) or electronic form 

(Figure 4), is the primary source of water quality 

information for the LTRMP, the importance 

of accuracy, legibility (paper version), and 

completeness cannot be overemphasized. Errors 

on the data sheet are difficult, and sometimes 

impossible, to detect and correct. If illegible 

or incorrect data are recorded, the time spent 

in the field may be totally wasted. Likewise, 

the laboratory resources spent analyzing any 

samples associated with incorrect field data are 

lost. Program resources, better used elsewhere, 

are also required to track down and correct 
61

Figure 4. Electronic water quality data sheet used by the Long Term Resource Monitoring Program. Table 12 

provides further descriptions of the numbered fields in this figure. 
62 

(if possible) data sheet errors. Errors that go 

undetected will eventually undermine the 

accuracy and credibility of the LTRMP.

 In 2001, the LTRMP deployed electronic data 

sheet software that intercepts the errors most 

commonly associated with field data recording 

and eliminates legibility issues, but the ultimate 

responsibility for obtaining and recording 

accurate monitoring data in the LTRMP still 

remains with the individual field team member. 

All field teams are to carefully examine data 

records before they are transmitted to the 

laboratory and database.

8.1 Sample Batches

 In LTRMP water quality monitoring, the 

term “sample batch” is used to describe samples 

and associated data that are collected within a 

short interval (e.g., a day or week) for a single 

sampling project and with a single sampling 

design (FSS , SRS, or special project). The 

temporal span of a batch is flexible; for example, 

an entire SRS episode, or a single day of 

sampling (SRS or FSS) could be processed as 

a single batch. However, a batch should never 

extend beyond a full SRS episode or an FSS 

period (e.g., a week), because this requires 

extended storage of samples before analysis. The 

ScanLog32 software does not impose any limit 

on the time span of a batch, but it will not allow 

samples from differing projects or sampling 

designs (SRS vs. FSS) to be combined into a 

single batch.

8.2 Crew Leader and Recorder Codes

 Because the individual field team leader or 

member has ultimate control over the quality 

of data obtained in the LTRMP, the individuals 

who lead the field team and record the data are 

assigned a unique code. This code is recorded 

on each data sheet for which the individual is 

responsible (either as a team leader or a data 

recorder). The code is assigned by the LTRMP 

database administrator and is permanently 

associated with an individual. It is not transferred 

to another employee or reused after an employee 

leaves the Program.

8.3 Data Sheet Description

 The water quality data sheet (Appendix J) 

was substantially revised in June 1993, 

additional minor changes were made in July 

1999, and conversion to an electronic version 

was completed in July 2001 (Appendix J). The 

1993 revision included several major changes: 

(1) use of bar code labeling (see above), 

(2) Quality Factor (QF) codes for each data 

item, (3) use of wave height codes, (4) recording 

of substrate information, (5) recording of 

vegetation information, (6) optional recording 

of geographic position, (7) recording of samples 

submitted for analysis, (8) allowance for up 

to six sample depths (or sample types) per 

site, and (9) allowance for QA/QC tests to be 

assigned. The previously recorded depth code 

was eliminated from the data sheet as this 

classification can be readily derived from sample 

and water depth as needed. The next revision 

(1999) included an additional sample row (for 

a total of seven), updated the quality factor 

information, added a provision for recording 

the monitoring instrument serial number, added 

a capability for using an additional bar code to 

link the data sheet to other projects or LTRMP 

components, and corrected a few minor errors.

 This section provides description and 

instructions on the use of the data sheet 

(Figure 4 and Table 12). Detailed descriptions 

of parameters and methods are provided in other 

sections.

8.4 Use of Quality Factor Codes 

 Most fields on the water quality data sheet 

have associated QF codes that can be assigned to 

indicate problems or other special considerations. 

The electronic data sheet provides valid choices 

for the QF codes as pop-up or drop-down menu 

items. This section (Table 13) gives additional 

descriptions and guidance for the use of QF 

codes on the LTRMP water quality data sheet.
63

Table 12. Description of the Long Term Resource Monitoring Program (LTRMP) electronic water quality data sheet fields with instructions 

for use and reference to procedures that relate to the specific data sheet entry. Figure number references individual fields in Figure 4

Figure 

number Field label Description and coding instructions

Related

section(s)

1 Field station Numeric designator of field station

1 = Lake City, Minnesota

2 = Onalaska, Wisconsin

3 = Bellevue, Iowa

4 = Pool 26, Illinois

5 = Open River, Missouri

6 = Havana, Illinois

7 = Upper Iowa University

0 = UMESC, any location, special projects only

1.1

2 Location code ScanLog32 provides a drop-down menu of valid choices. See 

appropriate sections on fixed-site sampling (FSS) and stratified random 

sampling (SRS) site identifiers for the syntax of the location code. 

In SRS, the location code may have an optional AA@ suffix appended 

if it is an alternate site. A permanent location code dictionary is 

maintained in ScanLog32 for FSS (Appendix B). The SRS location 

code dictionaries (with associated coordinates and strata designations) 

are supplied quarterly by UMESC. See further instructions on the site 

comment field for documenting the use of alternate sites.

1.5, 1.6, 

Appendix B

3 MM DD YYYY Date of site visit. Format is MM/DD/YYYY. None

4 HH MM Time of site visit as central standard, 24-hour clock. At the user=s 

option, the electronic data sheet will fill this field automatically during 

data acquisition. Clicking on the small clock icon adjacent to these 

fields will update this field to the present clock time.

1.3

5 # Rows Number of samples (depths) collected at this location. Number must 

match the number of sample or depth rows filled out (maximum 

number of records is seven). This is filled automatically by the 

electronic data sheet and is not accessible to the user.

3.11

6 Project code Routine LTRMP sampling has an M project code; other codes used 

for special projects are obtained from the component coordinator as 

needed. This field is filled automatically by the electronic data sheet.

None

7 Sheet bar code On the paper version of the data sheet, a unique data sheet bar code is 

attached at this location. The electronic data sheet provides this label 

automatically or the user can manually enter a value. Note that the 

serial number used for the data sheet may also be used as a sample bar 

code. The sheet and sample serial numbers are independent series, but 

typically their use is closely coordinated so that the sheet bar code and 

the first sample bar code on the sheet are the same.

7.14

8 Z max Zmax is always measured as the vertical distance from the free 

(unconfined) surface of the water to the substrate. It is reported to the 

nearest 0.01 m, but in water >1 m deep the value can be rounded to the 

nearest 0.1 m.

3.1, Figure 2

9 Secchi Secchi disk transparency is measured to the nearest centimeter. It 

cannot exceed the value for Zmax (e.g., if Zmax = 1.10 m, then Secchi disk 

transparency cannot exceed 110 cm).

4.4, 4.7

10 Wave code Numeric code based on Beaufort Scale is entered here. Valid choices 

appear at the bottom of the paper data sheet and as a pop-up menu on 

the electronic data sheet.

3.4, Table 5
64 

Table 12. Continued.

Figure 

number Field label Description and coding instructions

Related

section(s)

11 Zice cm Ice depthCmeasured to the nearest centimeter. 3.2, Figure 2

12 Zsice cm The submerged thickness of the Zsice measured from the bottom of the 

ice to the water surface, rounded to the nearest centimeter.

3.2, Figure 2

13 % Ice Percent ice cover, rounded to the nearest 10%. If any ice less than 10% 

is present, a 1 is reported.

3.8.1

14 Zsnow Snow depth (Zsnow), measured to the nearest centimeter. 3.8.4

15 % Snow Percent snow cover, measured to the nearest 10%. If any snow less than 

10% is present, a 1 is entered.

3.8.5

16 Site type Indicates the type of sampling location (this field is filled in 

automatically by ScanLog 32):

0 = SRS primary site

1 = SRS alternate site

2 = FSS site

3 = Other type of sampling site

1.5, 1.6, 1.7, 1.8

17 Summary code Specifies a condition that is applicable to all measurements taken at 

the site. This field was not used as of date of publication. Valid choices 

appear as a pop-up menu on the electronic data sheet and include:

Blank = Site is OK, same as code A5@

0 = Reserved for future use

1 = Obsolete (one or more of the data values for this site are suspected 

or known to be in error)

2 = Obsolete (possible equipment malfunction) replaced by individual 

quality factor (QF) codes

3 = Obsolete (site probably nonrepresentative because of local, 

short-term conditions)

4 = Obsolete (data analysis suggests the observation is atypical, but no 

reporting or transcription errors have been identified)

5 = Same as blank entry

6 = Site frozen to bottom, or close enough to prevent sample collection

7 = Site too shallow to sample

8 = Site dry (dewatered), 7 is implied

9 = Site inaccessible (and not 7 or 8)

7.1, 7.5

18 Substrate Measured at least once per quarter at all sites in shallow, low-velocity 

areas (i.e., contiguous backwaters). Optionally measured at other 

locations. Grabs or other suitable surficial samples are used to make the 

determination. 

This measurement is required in backwaters only, but at the discretion 

of the field team these measurements can also be made in channels. In 

FSS (other than channel sites), measurements are made at least once 

per quarter. They are required in backwaters during all SRS episodes.

3.9

19 Veg cover A one-digit approximation of aquatic vegetation coverage within the 

sampling radius of the sampling location. Valid entries are listed on 

the data sheet or as pop-up menu items on the electronic data sheet. A 

value is recorded at every site visit.

0 = 0%

1 = 1B19%

2 = 20B49%

3 = >50%

3.10.1
65

Table 12. Continued.

Figure 

number Field label Description and coding instructions

Related

section(s)

20 Veg density A one-digit semiquantitative assessment of stem concentration within 

the sampling radius of the sampling location. Valid entries are listed on 

the data sheet and as pop-up menu items on the electronic data sheet. 

Recorded at every site visit, but left blank if no vegetation is present. 

Note the difference between veg cover and veg density. An area can be 

completely covered with a sparse stand of vegetation (e.g., Nelumbo).

1 = Sparse

2 = Dense

3.10.2

21 Veg type The type(s) of vegetation present in the immediate sample area. Valid 

entries are listed on the data sheet and as pop-up menu items on the 

electronic data sheet. Left blank if no vegetation is present.

 S = Submergent

 E = Emergent

 F = Floating

 B = Two or more of the above categories

 C = Combination of S, E, or F 

3.10.3

22 Cross-link bar 

code

Optional field provided to link the data sheet to other projects or data. 

This identifier should also appear on the data sheet(s) from the other 

project(s) to which it is linked.

None

23 Method Indicates the method used to locate sampling sites. This field is used 

only for special projects where sampling locations are determined 

in the field rather than from predefined sampling locations. This is 

frequently used in the LTRMP fish component, but not water quality. 

As of September 28, 2000, a 1 is the default provided by ScanLog32 

and is the only valid entry.

1.4

24 Zone Universal Transverse Mercator (UTM) grid zone used to determine 

easting and northing coordinates (see next two fields)

1.4

25 Coordinates 

(East/West)

UTM coordinate east of the reference meridian. Not used in routine 

monitoring, but available for special projects to record field-obtained 

site coordinates.

1.4, 1.6

26 Coordinates 

(North)

UTM coordinate north of the reference parallel. Not used in routine 

monitoring, but available for special projects to record field-obtained 

site coordinates.

1.4, 1.6

27 Accuracy This field was intended originally to record the accuracy of global 

positioning system or other positioning system coordinates. It is not 

used for routine monitoring, but is available for use in special projects.

None

28 Field derived 

stratum

Describes the stratum in which an SRS site is actually found if it 

differs from the original designation. Valid choices appear on the 

paper data sheet and as a pop-up menu on the electronic data sheet. 

This designation is recorded in the LTRMP database as Afield derived 

stratum.@ It is used in data interpretation, but it is not used for updating 

the base map or modifying the stratum code assigned to the geographic 

coordinates of this location.

1.6
66 

Table 12. Continued.

Figure 

number Field label Description and coding instructions

Related

section(s)

29 Sample type Indicates whether routine or Quality Assurance and Quality Control (QA/

QC) sampling is reported on this data sheet. Blank field or zero indicates 

routine sampling, 1 indicates QA/QC sampling, and that the QA/QC 

categories are applicable to the reported sample rows.

2.1.1, Table 4

30 Instrument 

code

The serial number (or other unique identifier) of the multiparameter 

instrument used to obtain readings in the sample rows. The electronic 

data sheet automatically carries this identifier forward to new sheets.

2.2

Appendix D

31 Recorder code Three character identifier (normally numeric) for the individual who 

records the field data. Each field team member obtains this unique 

identifier from the LTRMP database administrator. It is not shared or 

reused.

8.2

32 Crew leader 

code

Three-character identifier for the individual leading the field team. Each 

individual field team member obtains this unique identifier from the 

component coordinator.

8.2

33 Site comments Also called station commentsCcontains up to 80 characters of general 

site observations. No punctuation (commas, ampersands, or quotes) may 

be used in this field. An entry is required in this field if no depth rows 

are filled (# rows = 0), if a turbidity sample was diluted for analysis 

(ScanLog32 inserts comment automatically), or an alternate SRS site is 

being sampled. If an alternate site, then comments should indicate the 

original site that is being replaced. A comment should also be recorded 

on the sheet associated with the inaccessible or unsuitable primary SRS 

site.

34 Z Sample depth in meters, recorded to the nearest 0.01 m when <1 m; and 

to the nearest 0.1 m when 1 m.

3.1

35 Temp Water temperature to the nearest 0.1C. Note that small negative values 

(-0.1 to -0.2) are possible.

4.6

36 DO Dissolved oxygen concentration to the nearest 0.1 mg/L. Values above 

instrument limits (e.g., 25 mg/L) must be accompanied by a QF code of 2 

(off-scale high).

5.6

37 pH pH to the nearest 0.1 pH unit. 4.2

38 Cond Conductivity (also called specific conductance) to the nearest whole 

S/cm.

4.1

39 Turb Nephelometric turbidity unit (NTU; to the nearest whole NTU). This 

value is derived from raw instrument NTU (next field) and is the same 

as the raw reading if that is less than 100 NTU. Raw samples that exceed 

100 NTU are diluted with deionized water to read within the 30 to 

50 NTU range. The dilution factor is then applied to estimate the original 

NTU. Record a QF code of 8 (sample diluted) for this field when dilution 

is required.

4.4, 4.5, 4.7

Appendixes D 

and J

40 Raw NTU Nephelometric turbidity (to the nearest whole NTU) as read from the 

field turbidimeter. A QF code of 8 (sample diluted) is only applied to 

this value if the raw value is >1,000 NTU and could not be read without 

dilution.

4.7

Appendixes D 

and J
67

Table 12. Continued.

Figure 

number Field label Description and coding instructions

Related

section(s)

41 Vel Horizontal speed of water current (m/sec) to the nearest 0.01 m/sec. 

If QF code of C (category measure) is used, this is a flow category 

measurement (numeric code from 0 to 6).

3.5, 3.6, 7.4

Appendix D

42 Dir The magnetic compass direction from which water is flowing past the 

sampling point, rounded to the nearest 10. If velocity is 0.02 m/sec, 

this reading is optional and may be left blank with a QF code of X 

(parameter optional) or 3 (reading off-scale, low).

3.7

43 Sample 

Bar code

A sample bar code is placed here if any laboratory samples are 

submitted for this row. This block is left blank if no samples are 

submitted. For the first sample row on a data sheet, the sample bar code 

is usually the same as the data sheet bar code. Sample bar codes are not 

typically assigned during data acquisition in the field, but rather when 

samples are being processed for shipment to the LTRMP laboratory. 

The electronic data sheet will assign the sample bar code automatically 

if the user requests it.

7.15

44 Filtered 

and Unfilt. 

(chemical 

sample codes)

QF code is entered to indicate type and condition of samples collected 

for submission to the laboratory. Blank indicates sample not submitted 

(QF code of 5 indicates that a normally submitted sample was 

unobtainable or lost before submission).

2.3,8.4, 

Table 13

45 QA/QC 

sample types

This column provides guidance as to what type of QA/QC sample 

is reported on each row when the sample type = 1 (QA/QC). On the 

electronic data sheet, these labels are enabled only when sample 

type = 1 (QA/QC).

2.1.1

46 Tare/Serial Electronic data sheet or electronic custody sheet only. This is the tare 

weight (five digits without the leading decimal) or five-character serial 

number from the planchet label or laboratory bar code. This value is 

usually entered when samples are being prepared for shipment, rather 

than during field data acquisition.

4.5, 7.8.5, 7.14

47 Vol (mL) Volume (mL) filtered for suspended solids or spectrophotometric 

chlorophyll-a (CHLS). Entered on the electronic data sheet or 

electronic custody sheet only. Volumes are usually entered when 

samples are being prepared for shipment, rather than during field data 

acquisition.

4.5, 6.1, 7.8.5, 

7.14

48 QF Most fields on the data sheet have an associated QF code. Valid 

choices are listed at the bottom of the paper sheet and appear as pop-up 

menu items on the electronic data sheet. Unless a problem or special 

condition exists, the QF code is left blank.

2.3, 4.4, 

4.7, 5.6, 8.4, 

Table 13

49 Sample 

comment

Electronic data sheet only. This provides the option of adding a samplespecific comment to the data sheet. This comment is not restricted 

in length (several hundred characters can be easily handled) nor in 

punctuation. Currently, these comments are stored in the laboratory 

database only, not the central LTRMP database.

8.6
68 

Table 13. Description of water quality data sheet quality factor codes used in the Long Term Resource Monitoring Program.

Quality 

factor 

code Description

Cross 

reference

Blank No problems and no exceptional circumstances. When used as a sample 

submission code, this indicates no sample submitted.

Appendix C

0 Equipment inoperative. Equipment will not function or function is so intermittent 

or erratic as to render data unusable. Conditions that prohibit operation are 

covered under quality factor (QF) code of 5.

Appendix C

1 Equipment questionable. Measurement is reasonable and probably correct, but 

intermittent, erratic, or erroneous instrument behavior was noted immediately 

before or after the measurement.

Appendix C

2 Reading off-scale (too high). Actual value was too high for the instrument to 

measure (not an instrument error). The instrument’s maximum value is recorded. 

A negative sign is not used, but a QF code of 2 must be recorded.

3 Reading off-scale (too low). Actual value was too low for the instrument to 

measure (below detection or negative; instrument function is normal). The lower 

limit of the instrument is recorded. A negative sign is not used on the data sheet. 

A QF code of 3 must be recorded.

4 Sample returned to laboratory for processing. This indicates that because of 

instrument or field conditions, an in situ measurement was not taken, but the 

sample was returned to laboratory for measurement or processing. This QF code 

applies only to samples that are normally processed or measured in the field. 

For turbidity readings, this code is not appropriate if the determination is made 

within 24 hours of sample collection.

Section 7.8.2

5 Sample unusable or unobtainable. This code provides explanation for missing 

data at a site. Additional site comments are required. If a sampling site is 

inaccessible so that no data can be obtained, this is indicated by absence of data 

rows (data sheet NROWS field is 0) and an appropriate site comment.

Sections 1, 7.5

6 Sample not representative of ambient conditions. The best sample that could 

be obtained may not reflect general conditions at the site. The quality of the 

sample is questionable, but is probably OK. Use QF code of 7 if the problem is 

contamination. If the sample is obviously unsuitable, then another sample should 

be taken or QF code of 5 should be used if a sample cannot be obtained. If this 

condition applies to the site in general, an appropriate site summary code should 

also be recorded (Table 12).

Section 2.3, 

Table 12

7 Sample possibly contaminated. It is likely, but not certain, that foreign material 

has entered the sample bottle. Additional explanation in the site comment is 

recommended. This QF code is generally used only for samples that are returned 

to the laboratory for analysis.

Section 2.3, 

Table 12

8 Sample diluted for analysis (i.e., for turbidity measurement). This QF code is 

used exclusively for turbidity measurements. The dilution volumes and resulting 

factors are recorded in the sample comments. This QF code usually applies only 

to the calculated turbidity value that results from dilution; it is not used to flag 

the original raw nephelometric turbidity unit (raw NTU) instrument reading from 

which the diluted reading was derived, unless readings are above 1,000 NTU, and 

dilution is required to obtain a reading.

Section 2.3, 

Table 12

9 Not used. None
69

8.5 Data Sheet Submission

 As of July 2001, LTRMP water quality data 

sheets are submitted electronically from the 

field station over the Internet directly to the 

LTRMP analytical laboratory with software 

(ScanLog32) developed by D. M. Soballe of the 

Upper Midwest Environmental Sciences Center 

(UMESC). Following laboratory processing, 

data sheet information is transmitted from 

the laboratory to the main LTRMP database. 

Before July 2001 and during a transition period 

extending from July 2001 to December 30, 2001, 

paper data sheets were submitted by the field 

station teams to a data entry contractor following 

instructions provided by the LTRMP database 

administrator. 

 The ScanLog32 software includes sample 

custody information automatically in its 

electronic transmission from the field station, 

but from October 1995 to July 2001, electronic 

custody records (DOS, ASCII text files with an 

extension of .lb2) were sent by e-mail manually 

to the LTRMP laboratory. Field stations maintain 

archive copies (both paper and electronic) of all 

data sheets submitted.

8.6 Electronic Data Acquisition

 Water quality monitoring in the LTRMP 

produces a large volume of field data (6,000 data 

sheets) and samples (20,000 containers) each 

year. To process this material efficiently, the 

LTRMP staff uses an automated system of data 

and sample management that includes (1) field 

computers and customized software to acquire 

data from manual entries and instrument outputs 

and (2) a customized laboratory information 

management system (LIMS) that relies heavily 

on bar codes to track samples and analytical 

results through the system. 

 As of July 2001, field data in LTRMP water 

quality monitoring are subjected to extensive 

real-time syntax and contextual checking as 

they are acquired in an electronic data sheet. 

This is accomplished using a software package 

(ScanLog32) that water quality teams run on a 

notebook computer while (1) in the field at the 

sampling location and (2) at the field station 

when processing samples for shipment to the 

laboratory. The software produces data and 

custody records that are sent electronically to 

the LTRMP analytical laboratory LIMS and are 

printed at the field station for archival purposes. 

The LIMS uses the electronic records (and bar 

code labels) to identify samples, track custody, 

and to guide and monitor analytical processing. 

After laboratory processing, the software 

forwards the electronic data sheets from the 

LIMS to the central LTRMP database.

 The electronic version of the data sheet 

maintains the familiar “look and feel” of the 

paper version (Figure 4). This avoids much of 

the disruption related to retraining and relearning 

and also eliminates the need for radical changes 

in the established data management process. It 

Table 13. Continued.

Quality 

factor

code Description

Cross 

reference

A Nonstandard (alternative) method used for collection or processing of sample 

or measurement. Some innovative technique was needed to obtain a suitable 

sample or measurement. Additional explanation in site comment is required.

Sections 3.5, 3.6, 4.5, 

4.7, 5.6

C Category measurement is being used (i.e., for current velocity measurement). Section 3.6

D Instrument calibration is out of limits. Appendix C

F Operator error resulted in missed or unusable value.

H Sample holding time exceeded.

X Optional measurement not performed, or measurement is not applicable.
70 

also allows archives based on paper records to be 

continued without significant change.

 Error trapping was the primary goal in 

implementing an electronic data sheet for 

LTRMP water quality monitoring; rugged 

computers and customized software provide 

the field teams with real-time detection and 

correction of errors as data are acquired. 

Although error rates were low before the use of 

the electronic data sheet (on the order of 1–2 per 

1,000 keystrokes), data volume is large (greater 

than 500,000 keystrokes per year) and after-thefact detection and correction are extremely costly 

(0.25 to 1.5 hours per error).

 The ScanLog32 software uses two levels of 

real-time error checking to produce extremely 

low error rates (less than 1 per 10,000 keystrokes) 

in data that enter the data management process: 

(1) syntax checks are performed as data are 

entered into each field of the data sheet to 

ensure that the entry is properly formatted (valid 

numeric value with correct precision, etc.) and 

that the properly formatted value is in the range 

allowable for the geographic area and month 

of the year, and (2) more sophisticated context 

checks are performed when each data sheet is 

completed to ensure that all the required fields 

are filled and that all entries are consistent with 

each other and with the procedures established 

in this manual (e.g., Secchi disk transparency 

or sampling depth cannot exceed maximum 

depth of the water column; nontributary sites 

with current velocity <0.1 m/s and available 

water depth >0.6 m require near-bottom readings 

of temperature, pH, dissolved oxygen, and 

conductivity; snow cover cannot be present in the 

absence of ice cover; vegetation type cannot be 

specified when vegetation cover is zero). Several 

hundred checks of this type are performed on 

each data sheet in a fraction of a second as the 

field team member completes the entries on the 

form. These checks were developed in close 

collaboration with field team members and 

they incorporate much of the error detection 

experience and expertise accumulated by the field 

team members over the years.

 When the software encounters an invalid or 

missing entry, it gives the operator an immediate 

indication and diagnosis of the problem. The 

application’s help utility, of particular value to 

less-experienced field technicians, provides direct 

access to the relevant sections of this manual.

 ScanLog32 provides several documentation 

capabilities that are not available on the paper 

version of the data sheet. With ScanLog32, the 

user can attach an extended textual comment 

to any individual sample. This comment is not 

restricted in length (several hundred characters 

can be easily handled) nor in punctuation. 

These individual sample comments are stored 

in the laboratory database only, not the central 

LTRMP database. A parallel capability allows 

the laboratory staff to attach another sample 

comment upon receipt of the sample at the 

laboratory. ScanLog32 provides an electronic 

notepad (field log) that can be used by the field 

teams for recording information that is not 

forwarded to the laboratory. The field teams 

may also set (or clear) reminders that appear 

automatically whenever the user reopens a 

sample batch for processing with ScanLog32.

 Detailed descriptions of the ScanLog32 

software and its use in LTRMP water quality 

operations are provided in separate software 

documentation.

8.7 Archival Storage of Data 

and Associated Records 

 The long-term value of the LTRMP depends 

on the data acquired by this program being 

available to users in future decades or beyond. 

It is essential that at least one method, not 

heavily reliant on advanced technology, exists to 

check and reconstruct the database maintained 

at UMESC. The LTRMP uses archived paper 

copies of the data sheets held at the separate field 

stations and at UMESC for this purpose. Copies 

in multiple locations ensure that LTRMP archives 

are never completely lost because of a localized 

event (fire, flood, other) or data system failure. 

After December 2001, the archival process was 

streamlined, with an original certified paper 

copy of each data sheet maintained only at the 

originating field station, and electronic copies on 

multiple media (compact disk, magnetic disk) as 

ASCII text files held at the UMESC laboratory 

and by the UMESC database administrator. The 
71

content of these ASCII files is also printed out 

in a condensed format for archival storage by 

UMESC.

 Additional records associated with water 

quality monitoring in the LTRMP (e.g., 

equipment maintenance logs, field notebooks) are 

held in safe locations at each of the field stations. 

9. Acknowledgment

 The authors of this manual have compiled 

and edited information provided by numerous 

water quality professionals associated with 

the Long Term Resource Monitoring Program 

from 1988 to 2003. These individuals provided 

technical information, as well as review 

comments and suggestions on a series of drafts 

that have led to this version of the manual. 

Without the contributions from the following 

individuals, several of whom have now moved 

to new positions, this manual could not have 

been completed: Robert Burdis, Minnesota 

Department of Natural Resources, Lake City, 

Minnesota; Kraig Hoff, Kevin Mauel, Troy 

Clemment, and Lisa Hodge-Richardson, 

Wisconsin Department of Natural Resources, 

Onalaska, Wisconsin; Lesly Conaway, Jennifer 

Frazier, David Herzog, and David Ostendorf, 

Missouri Department of Conservation, Jackson, 

Missouri; David Gould and Michael Steuck, 

Iowa Department of Natural Resources, Bellevue, 

Iowa; Eric Ratcliff, Brian Macias, and Mack 

Sitzes, Illinois Natural History Survey, Brighton, 

Illinois; and Jeff Arnold, Doug Blodgett, Steven 

Stenzel, and Rick Wright, Illinois Natural 

History Survey, Havana, Illinois. Our sincere 

thanks, and those of our Program partners and 

collaborators, are extended for their dedication 

and all-important contributions to the Long Term 

Resource Monitoring Program on the Upper 

Mississippi River System and to this manual.

10. References

APHA (American Public Health Association). 

1992. Standard methods for the examination of 

water and wastewater. 18th edition. American 

Public Health Association, Washington, D.C. 

Various pages.

APHA. 1998. Standard methods for the 

examination of water and wastewater. 20th

edition. American Public Health Association, 

Washington, D.C. Various pages + 10 sections, 

color plates, and index

Cole, G. A. 1979. Textbook of limnology. 2nd

edition. The C. V. Mosby Company, St. Louis, 

Missouri. 426 pp.

Hydrolab Corporation. 1991a. DataSonde3, 

multiparameter water quality datalogger 

operating manual. Hydrolab Corporation, 

Austin, Texas. 83 pp.

Hydrolab Corporation. 1991b. Performance 

manual for field water quality instrumentation. 

Hydrolab Corporation, Austin, Texas. 28 pp.

Hydrolab Corporation. 1997. DataSonde4 and 

MiniSonde water quality multiprobes, users 

manual. Hydrolab Corporation, Austin, Texas. 

HL#003078, Revision D, August 1997. 

Various pages + 7 sections and 5 appendixes.

Hynes, H. B. N. 1970. The ecology of running 

waters. University of Toronto Press, Toronto, 

Canada. 555 pp.

Imlay, M., 1973. Effects of potassium on survival 

and distribution of freshwater mussels. 

Malacologia 12:97-113.

Lind, O. T. 1979. Handbook of common methods 

in limnology. 2nd edition C. V. Mosby 

Company, St. Louis, Missouri. 199 pp.

Lubinski, K. S., and J. L. Rasmussen. 1988. 

Procedures manual of the Long Term Resource 

Monitoring Program for the Upper Mississippi 

River System. U.S. Fish and Wildlife Service, 

Environmental Management Technical Center, 

Onalaska, Wisconsin. EMTC 88-03. 216 pp. 

(NTIS # PB94-145885)

Marsh-McBirney, Inc. 1994. Flo-matetm model 

2000 portable water flow meter instruction 

manual. Marsh-McBirney, Inc., Frederick, 

Maryland. 20 pp.

Owens, T., and J. J. Ruhser. 1996. Long Term 

Resource Monitoring Program standard 

operating procedures: Aquatic areas database 

production. National Biological Service, 

Environmental Management Technical 

Center, Onalaska, Wisconsin, March 1996. 
72 

LTRMP 95-P008-6. 4 pp + Appendix 

(NTIS # PB96-172267)

Rogers, S. J., and T. W. Owens. 1995. Long Term 

Resource Monitoring Program procedures: 

Vegetation monitoring. National Biological 

Service, Environmental Management 

Technical Center, Onalaska, Wisconsin, 

July 1995. LTRMP 95-P002-3. 10 pp. + 

Appendices A–E

USEPA (U.S. Environmental Protection Agency). 

1974. Methods for chemical analysis of water 

and wastes. EPA-625/6-74-003. 298 pp.

U.S. Fish and Wildlife Service. 1993. Operating 

Plan for the Upper Mississippi River System 

Long Term Resource Monitoring Program. 

Environmental Management Technical 

Center, Onalaska, Wisconsin, Revised 

September 1993. EMTC 91-P002R. 179 pp. 

(NTIS #PB94-160199)

U.S. Geological Survey. 1999. National field 

manual for the collection of water-quality data: 

U.S. Geological Survey techniques of waterresources investigations. Book 9, chapters. 

A1–A9, 2 v., various pages. [Chapters were 

published from 1997 to 1999; updates and 

revisions are ongoing and can be viewed 

at: http://water.usgs.gov/owq/FieldManual/

mastererrata.html]

U.S. Naval Oceanographic Office. 1966. 

American practical navigator, an epitome 

of navigation. H. O. Publication 9. U.S. 

Government Printing Office, Washington, D.C. 

1,524 pp.

Welch, P. S. 1948. Limnological methods. 

Blaiston Company, Philadelphia. 381 pp.

Wetzel, R. G. 2001. Limnology. 3nd edition. 

Academic Press, San Diego. 1,006 pp.

Wetzel, R. G., and G. E. Likens. 1991. 

Limnological analyses. 2nd edition. SpringerVerlag, New York. 391 pp.

Wilcox, D. M. 1993. An aquatic habitat 

classification system for the Upper Mississippi 

River System. U.S. Fish and Wildlife Service. 

Environmental Management Technical Center, 

Onalaska, Wisconsin. May 1993. EMTC 

93-T003. 9 pp + Appendix A (NTIS #PB93-

208981)

Wlosinski, J. H., D. E. Hansen, and S. R. 

Hagedorn. 1995. Long Term Resource 

Monitoring Program procedures: Water 

surface elevation and discharge. National 

Biological Service, Environmental 

Management Technical Center, Onalaska, 

Wisconsin, August 1995. LTRMP 95-P002-4. 

9 pp. + Appendixes A–O

Yin, Y., J. S. Winkelman, and H. A. Langrehr. 

2000. Long Term Resource Monitoring 

Program procedures: Aquatic vegetation 

monitoring. U.S. Geological Survey, Upper 

Midwest Environmental Sciences Center, 

La Crosse, Wisconsin. April 2000. LTRMP 

95-P002-7. 8 pp. + Appendixes A–C 

11. Glossary

AWD Available water depth

BT Sample depth code for bottom 

sample

BOD Biochemical oxygen demand

Ca Calcium

CHLF Chlorophyll-a determined 

fluorometrically (F)

CHLS Chlorophyll-a determined spectroph

otometrically (S)

Cl Chloride

DI Deionized water

DIN Dissolved inorganic nitrogen

DKN Total dissolved Kjeldahl nitrogen

DMSO Dimethyl sulfoxide

DO Dissolved oxygen

Fe Iron

FSS Fixed-site sampling

FTP File transfer protocol

GIS Geographic information system

GPS Geographic positioning system

H2SO4 Sulfuric acid

HNO3 Nitric acid

HCl Hydrochloric acid

HgCl2 Mercuric chloride

JTU Jackson turbidity units

K Potassium

KCl Potassium chloride

LIMS Laboratory information management 

system

LTRMP Long Term Resource Monitoring 

Program

MD Sample deplth code for mid-depth 

sample
73

MET Dissolved metals sample used for 

cation determinations

Mg Magnesium

Mn Manganese

N Nitrogen

Na Sodium

NHx Ammonia plus ammonium

NIST National Institute of Standards

NOx Nitrate plus nitrite

NROWS Number of detail rows (depths) 

completed on the data sheet

NTU Nephelometric turbidity units

NVSS Nonvolatile suspended solids

OT Sample depth code for samples from 

other than surface, mid-depth, or 

bottom

QA/QC Quality assurance and quality control 

QF Quality factor 

P Phosphorus 

PAR Photosynthetically active radiation 

PVC Polyvinyl chloride 

RM River mile, measured upstream from 

the river mouth 

SF Sample depth code for surface 

samples

Si Silicate

SRP Soluble reactive phosphorus, 

dissolved reactive phosphorus, also 

the SRP-chloride sample bottle

SRPH Soluble reactive phosphorus 

(hydrolyzed by acid preservation) 

as determined on an acid-preserved 

sample 

SRS Stratified random sampling 

SO3 Sulfite

SO4 Sulfate

TDP Total dissolved phosphorus

TKN Total Kjeldahl nitrogen

TNP Total nitrogen and phosphorus 

sample container 

TSS Total suspended solids 

UMESC Upper Midwest Environmental 

Sciences Center 

UMRS Upper Mississippi River System

UTM Universal Transverse Mercator 

VSS Volatile suspended solids 

WDP Water depth, vertical thickness of 

the liquid layer of water between 

the substrate and the bottom of any 

overlying ice cover (obsolete)

Zmax Water depth, vertical distance 

between the substrate and the free 

surface of the water 

Z0 Water surface 

Zice Total vertical extent of ice, total ice 

thickness above and below water 

surface

Zsice Vertical extent of ice below the water 

surface, submerged ice thickness

Zsnow Vertical extent of snow cover 
A-1

Appendix A. Sampled Parameters and Sampling Frequencies

 This appendix provides a tabular listing of 

the parameters measured and the frequency of 

sampling in water quality monitoring of the Long 

Term Resource Monitoring Program (LTRMP).

A.1 Sample Parameters

A.1.1 Measurements Made In Situ or at Field 

Station

 This section summarizes the period of record 

for measurements made at the sampling site or on 

samples returned to the field station (Table A-1). 

Samples shipped to the analytical laboratory are 

described in Section A.1.2.

A.1.2 Samples Submitted to the Analytical 

Laboratory

 This section summarizes the period of 

record (Table A-2) and parameters measured 

(Table A-3) for samples shipped from the 

field to the analytical laboratory. Before 1994, 

chemical samples returned to the laboratory were 

analyzed at one of three sites: the U.S. Army 

Corps of Engineers Waterways Experiment 

Station facilities in Spring Valley, Wisconsin 

(Eau Galle Reservoir); the U.S. Army Corps 

of Engineers Waterways Experiment Station 

Facility in Vicksburg, Mississippi; or the Long 

Term Resource Monitoring Program (LTRMP) 

laboratory at the Upper Midwest Environmental 

Sciences Center in Onalaska, Wisconsin. 

All analyses were transferred to the LTRMP 

laboratory in 1994.

A.2 Sample Numbers and Frequency

 The number of samples collected for analysis 

and the frequency of water quality sampling in 

the Long Term Resource Monitoring Program 

has changed substantially over time in response 

to availability of funds and refinements in the 

Program objectives. These changes must be 

considered in the interpretation of long-term 

patterns or trends in the resulting data.

A.2.1 April 1991 Through April 1993

 Approximately 80–100 samples for chemical 

laboratory analyses were collected in fixedsite sampling (FSS) during each sampling 
A-2

week. Stratified random sampling (SRS) was 

not yet implemented. Chemical samples were 

collected biweekly from April through October 

(15–16 sampling dates) and every 4 weeks from 

November through March (5–6 sampling dates), 

for a total of 20–21 sampling dates per year. This 

produced approximately 1,800 total samples and 

29,000 total analyses per year.

A.2.2 June 1993 Through December 1999

 The list of FSS locations in each study reach 

was modified and the number of chemical 

parameters analyzed was reduced. In this 

revised design, the number of fixed sites was 

set at approximately 15 sites per field station, 

with biweekly collection of chemical samples. 

However, analysis of total soluble nitrogen, total 

soluble phosphorus, dissolved calcium, dissolved 

iron, and dissolved manganese were suspended 

in FSS pending the switch of analytical 

responsibilities to the LTRMP laboratory.

 The SRS was implemented in July 1993, 

with a full set of chemical parameters measured 

at only 50% of these quarterly SRS sites 

(120–150 per study reach). The SRS excluded 

total soluble phosphorus, total soluble nitrogen, 

dissolved calcium, dissolved iron, dissolved 

manganese, dissolved potassium, dissolved silica, 

and dissolved chloride. This eliminated two 

sample preparations (metals and total soluble 

nitrogen and phosphorus) during SRS. The 

reduced parameter list included all the usual in 

situ parameters (Table A-1) plus fluorometric 

chlorophyll-a and suspended solids.
A-3

Table A-3. Measurements performed on Long Term Resource Monitoring Program samples by participating laboratories. Each laboratory 

techniques are described in the procedures manuals for the Waterways Experiment Station (WES) Environmental Laboratory, and by the 

American Public Health Association et al. (1992). Values in parentheses represent the method detection limit.

Parameter and method

Laboratory

WESa-Vicksburg WES-EauGalle UMESCb

Total suspended solids:

Gravimetric/105 oC

– June 1991–June 1993

(1 g/L)

June 1993–Present

(1 g/L)

Volatile suspended solids:

Gravimetric/500 oC

– June 1991–June 1993

(1 g/L)

June 1993–Present

(1 g/L)

Chlorophyll-a: FluorometricDMSO-acetone extraction– – June 1993–Present

(1 g/L)

Chlorophyll-a: Spectrophotometric 90% acetone extraction– June 1991–June 1993

(1 g/L)

June 1993–Present

(1 g/L)

Total phosphorus: Automated/ 

persulfate/ascorbic acid

– June 1991– Jan. 1994

(1 g/L)

Jan. 1994–Present

(1 g/L)

Soluble reactive phosphorus 

(acidified, SRPH): Automated/ 

H2SO4 preservation, ascorbic acid

June 1991–Dec 1993

(1 g/L)

– –

Soluble reactive phosphorus:

Automated /frozen/ascorbic acid

Jan. 1994–Feb. 1994

(1 g/L)

– Feb. 1994–Present

(1 g/L)

Total soluble phosphorus: 

Automated/persulfate/ascorbic 

acid

– June 1991–Apr. 1993

(1 g/L)

–

Total nitrogen: Automated/

Devarda’s alloy

– June 1991–Jan. 1994

(0.01 mg/L)

Jan. 1994–July 1997

(0.01 mg/L)

Total nitrogen:

Persulfate digestion, automated 

cadmium reduction

– – March 1997–Present

(0.01 mg/L)

Total soluble nitrogen:

Automated/Devarda’s alloy

– June 1991–April 1993

(0.01 mg/L)

–

Nitrate and nitrite nitrogen: 

Automated Cd reduction

June 1991–April 1994

(0.01 mg/L)

April–June 1994

April 1997–Present

(0.01 mg/L)

Nitrate and nitrite nitrogen: Ion 

chromatography 

– – June 1994–Present

(0.01 mg/L)

Ammonia and ammonium: 

Automated salicylate

June 1991–Feb. 1994

(1 g/L)

– Feb. 1994–Present

(1 g/L)

Dissolved silicate silica: 

Automated/molybdate

June 1991–Feb. 1994

(0.01 mg/L)

– Mar. 1994–Present

(0.01 mg/L)

Sulfate: Ion chromatography – – Jan. 1994–Present

(0.1 mg/L) Dissolved chloride: Automated 

ferro-cyanide, ion

chromatography

June 1991–June 1994

Automated FeCN

(0.1 mg/L)

June 1994–Present

(0.1 mg/L)
A-4

A.2.3 January 1, 2000 Through September 2002

 Because of budget constraints, the design 

was modified to reduce overall sampling effort 

by 25–35%. Frequency of sampling in FSS was 

reduced from biweekly to once every 4 weeks, 

except for a few selected sites of special concern. 

The number of sites visited during SRS episodes 

was not changed, but the number of full-chemical 

sites was reduced from 50% to 33% of the total 

sites visited.

A.2.4 After September 2002

 The LTRMP water quality sampling was 

halted on September 30, 2002, in response to 

budget limitations. Reduced parameter sampling 

at a selected subset of fixed sites resumed in late 

April 2003. A return to the 2002 sampling level 

is proposed for January 2004.

Table A-3. Continued

Parameter and method

Laboratory

ESa-Vicksburg WES-EauGalle UMESCb

Dissolved calcium: Ion chromatography – – Jan. 1994–Present

(0.1 mg/L)

Dissolved calcium: Atomic 

absorption

June 1991–Oct. 1993

(0.1 mg/L)

– Oct. 1993–Jan. 1994

(0.1 mg/L)

Dissolved magnesium: Ion chromatographyJan. 1994 –Present

(0.1 mg/L)

Dissolved sodium: Ion chromatographyJan. 1994–Present

(0.1 mg/L)

Dissolved potassium: Atomic 

absorption

June 1991–Oct. 1993

(0.1 mg/L)

– Oct. 1993–Present

(0.1 mg/L)

Dissolved iron: Atomic absorptionJune 1991–Apr. 1993

(0.01 mg/L)

– –

Dissolved manganese: Atomic 

absorption

June 1991–Apr. 1993

(0.01 mg/L)

– –

a

WES=Waterways Experiment Station
B-1

Appendix B. Fixed-site Sampling Locations

Table B-1. Descriptions of fixed-site water quality sampling locations monitored by LTRMP staff from 1988 through September 2002. Period of record inot all sites were monitored as of the p 

Field

station State River name

River mile

Location codea

UTM zone Northing Easting

Habitat classb Additional comments

Fisa

1 WI Chippewa 0.1 CH00.1M 15 4917624 572933 TRIB mid-stream 011 MN Cannon 0.1 CN00.1M 15 4938767 532272 TRIB mid-stream 011 MN-WI Mississippi 738.2 M738.2F 15 4890151 595044 MC tailwater west side 051 MN-WI Mississippi 738.2 M738.2M 15 4890323 595248 MC tailwater mid-stream 011 MN-WI Mississippi 738.2 M738.2T 15 4890529 595380 MC tailwater east side 011 MN-WI Mississippi 742.6 M742.6B 15 4894604 589536 SC Weaver Bottoms outlet 041 MN-WI Mississippi 742.8 M742.8D 15 4894957 589565 SC Weaver Bottoms outlet 041 MN-WI Mississippi 743 M743.0E 15 4895083 589464 BWC Weaver Bottoms outlet 121 MN-WI Mississippi 745.2 M745.2L 15 4898404 589565 SC Weaver Bottoms inlet 041 MN-WI Mississippi 746.9 M746.9Y 15 4901280 589372 SC Weaver Bottoms inlet 041 MN-WI Mississippi 747.3 M747.3R 15 4901328 587763 SC Murphy’s Cut 041 MN-WI Mississippi 752.8 M752.8M 15 4908232 585992 MC LD 4 tailwater mid-stream 011 MN-WI Mississippi 752.8 M752.8Y 15 4908119 585823 MC LD 4 tailwater west side 041 MN-WI Mississippi 752.8 M752.8Z 15 4908276 586174 MC LD 4 tailwater east side 041 MN-WI Mississippi 753.1 M753.1X 15 4908533 585096 BWC Peterson Lake mouth 041 MN-WI Mississippi 753.2 M753.2S 15 4908555 583985 IMP Peterson Lake 011 MN-WI Mississippi 753.2 M753.2V 15 4908931 584545 IMP Peterson Lake 011 MN-WI Mississippi 757.2 M757.2Z 15 4914360 582462 BWC Big Lake mouth 041 MN-WI Mississippi 757.4 M757.4O 15 4912312 580808 BWC Robinson Lake 041 MN-WI Mississippi 757.5 M757.5O 15 4912238 580650 BWC Robinson Lake 041 MN-WI Mississippi 758.6 M758.6X 15 4915943 581454 BWC Big Lake 021 MN-WI Mississippi 758.6 M758.6Y 15 4915699 581212 BWC Big Lake 021 MN-WI Mississippi 760.7 M760.7O 15 4915321 576401 MC west side of channel wing dam 011 MN-WI Mississippi 761.5 M761.5E 15 4916388 575460 MC west side of channel 011 MN-WI Mississippi 764.3 M764.3A 15 4917826 571635 MC mid-stream 04
B-2

Table B-1. Continued.

Field

station State River name

River mile

Location codea

UTM zone Northing Easting

Habitat classb Additional comments

Firsa

1 MN-WI Mississippi 764.8 M764.8G 15 4918870 570994 BWI Isolated backwater 021 MN-WI Mississippi 766 M766.0B 15 4917935 568732 IMP-L Lake Pepin east side 011 MN-WI Mississippi 766 M766.0I 15 4919038 568951 IMP-L Lake Pepin mid-stream 011 MN-WI Mississippi 766 M766.0O 15 4920225 569220 IMP-L Lake Pepin west side 011 MN-WI Mississippi 771.2 M771.2P 15 4921651 561539 IMP-L Lake Pepin mid-stream 041 MN-WI Mississippi 775.6 M775.6L 15 4924953 555572 IMP-L Lake Pepin west side 011 MN-WI Mississippi 775.6 M775.6Q 15 4925675 556373 IMP-L Lake Pepin mid-stream 011 MN-WI Mississippi 775.6 M775.6Y 15 4926279 557162 IMP-L Lake Pepin east side 011 MN-WI Mississippi 781.2 M781.2E 15 4932250 551514 IMP-L Lake Pepin west side 011 MN-WI Mississippi 781.2 M781.2O 15 4933885 551416 IMP-L Lake Pepin mid-stream 011 MN-WI Mississippi 781.2 M781.2X 15 4935516 551310 IMP-L Lake Pepin east side 011 MN-WI Mississippi 786.1 M786.1S 15 4935869 543794 IMP-L Lake Pepin Bay City flats 011 MN-WI Mississippi 786.2 M786.2C 15 4934266 543779 MC mid-stream 041 MN-WI Mississippi 786.5 M786.5D 15 4934745 542976 SC Wisconsin channel mid-stream 041 MN-WI Mississippi 787.9 M787.9H 15 4935522 540890 BWC Dead Slough Lake 041 MN-WI Mississippi 790.3 M790.3F 15 4935661 537282 BWC Mud Lake 011 MN-WI Mississippi 792.5 M792.5N 15 4936971 536344 SC Wisconsin channel west side 111 MN-WI Mississippi 793.9 M793.9P 15 4938355 534406 MC west side of channel 011 MN-WI Mississippi 795.8 M795.8L 15 4938922 532288 BWI Isolated backwater 021 MN-WI Mississippi 796.7 M796.7M 15 4939642 531626 MC west side of channel wing dam 011 MN-WI Mississippi 796.9 M796.9M 15 4939664 531047 MC tailwater west side 041 MN-WI Mississippi 796.9 M796.9N 15 4939807 531001 MC tailwater east side 111 MN Vermillion 0.1 VM00.1M 15 4938817 532303 TRIB mid-stream 011 MN Wells Creek 0.8 WC00.8M 15 4928802 553735 TRIB mid-stream CO 2 bridge 011 MN Whitewater 1.3 WW01.3M 15 4895406 586129 TRIB mid-stream HWY 61 bridge 041 MN Zumbro 0.1 ZM00.1M 15 4904640 585582 TRIB mid-stream 042 WI Black 1 B001.0N 15 4855524 640507 TRIB Under Clinton St. Bridge 06
B-3

Table B-1. Continued.

Field

station State River name

River mile

Location codea

UTM zone Northing Easting

Habitat classb Additional comments

Fisa

2 WI Black 1 BK01.0M 15 4855524 640611 TRIB Fishing pier 12 m off-shore Copeland 

Park

06

2 WI Black 14.2 BK14.2M 15 4868518 633202 TRIB Mainstem Black at bike bridge Lytles 

landing enters Pool 7 near RM 708

05

2 WI Bad Axe 0.4 BX00.4M 15 4820006 644226 TRIB mid-stream HWY 35 bridge enters 

pool 9 near RM 675.3

06

2 WI Coon Creek 0.6 CC00.6M 15 4834061 643626 TRIB mid-stream HWY 35 bridge enters 

Pool 8 near RM 684.5

05

2 WI Coon Creek 4.6 CC04.6M 15 4834750 647900 TRIB mid-stream temporary exploratory site 

enters Pool 8 near RM 684.5

0

2 WI La Crosse 0.1 LX00.1M 15 4853086 640435 TRIB bike bridge north side of side Park 

enters Pool 8 RM 698.1

06

2 MN-WI Mississippi 679.5 M679.5V 15 4825913 642609 IMP west side of channel 072 MN-WI Mississippi 679.5 M679.5W 15 4825899 642742 MC high flow transect site 052 MN-WI Mississippi 679.5 M679.5X 15 4825899 642816 MC transect site-mid channel 02 MN-WI Mississippi 679.5 M679.5Y 15 4825899 642890 MC high flow transect site 052 MN-WI Mississippi 679.5 M679.5Z 15 4825899 642964 MC transect site-east side 02 MN-WI Mississippi 680.8 M680.8M 15 4828251 641268 IMP West side lower Pool 8 072 MN-WI Mississippi 680.8 M680.8U 15 4828329 642397 IMP lower Pool 8 072 MN-WI Mississippi 681.3 M681.3B 15 4828911 639935 IMP Reno Spillway 052 MN-WI Mississippi 684.8 M684.8W 15 4834212 643275 BWI Isolated backwater S of Stoddard 02 MN-WI Mississippi 684.8 M684.8Y 15 4836629 724102 BWI Isolated backwater S of Stoddard 02 MN-WI Mississippi 685 M685.0D 15 4833329 639806 BWC Raft Channel S of Brownsville 072 MN-WI Mississippi 685 M685.0E 15 4833364 639859 BWC Raft Channel S of Brownsville 072 MN-WI Mississippi 685.9 M685.9L 15 4835599 641380 MC Coon Slough 072 MN-WI Mississippi 685.9 M685.9M 15 4835529 641422 MC Coon Slough 072 MN-WI Mississippi 686.1 M686.1V 15 4836515 642600 BWC West side of Stoddard Bay 072 MN-WI Mississippi 686.4 M686.4K 15 4844362 641015 BWC Grassy Island 102 MN-WI Mississippi 686.6 M686.6J 15 4836021 640620 MC Turtle Island 072 MN-WI Mississippi 687.6 M687.6F 15 4836807 639637 BWC Inside Horseshoe HREP 07
B-4

Table B-1. Continued.

Field

station State River name

River mile

Location codea

UTM zone Northing Easting

Habitat classb Additional comments

Fs

2 MN-WI Mississippi 687.6 M687.6G 15 4836889 639753 BWC Inside Horseshoe HREP 02 MN-WI Mississippi 687.8 M687.8X 15 4837376 642793 BWC Crosby Slough NW side of Stoddard 

Islands

1

2 MN-WI Mississippi 689.2 M689.2A 15 4839410 639381 MC Main Ch border 12 MN-WI Mississippi 689.2 M689.2B 15 4839595 639543 MC MC border 02 MN-WI Mississippi 690.2 M690.2A 15 4841764 639243 BWC Lawrence Lake Marina 02 MN-WI Mississippi 690.4 M690.4A 15 4841500 639254 BWC Lawrence lake Marina 02 MN-WI Mississippi 690.8 M690.8B 15 4842150 639331 BWC Lawrence Lake mouth (channel to 

upper lake)

0

2 MN-WI Mississippi 691.3 M691.3B 15 4843204 639442 BWC Lawrence Lake 02 MN-WI Mississippi 691.6 M691.6E 15 4843992 640839 MC CBW East Of Lawrence Lake 02 MN-WI Mississippi 691.7 M691.7S 15 4843457 643127 BWI Goose Island near culverts under 

entrance road

0

2 MN-WI Mississippi 691.7 M691.7T 15 4843442 643215 BWI Goose Island near culverts under 

entrance road

0

2 MN-WI Mississippi 691.9 M691.9B 15 4843912 639676 BWC Mid-Lawrence Lake 02 MN-WI Mississippi 692.5 M692.5C 15 4845860 639855 BWC upper-Lawrence Lake 02 MN-WI Mississippi 692.7 M692.7R 15 4844961 642904 BWC North Goose Island landing 02 MN-WI Mississippi 692.8 M692.8P 15 4844944 641981 BWC Goose Island near culverts under road 02 MN-WI Mississippi 692.8 M692.8Q 15 4844887 642052 BWC Goose Island 02 MN-WI Mississippi 694 M694.0N 15 4847065 642510 SC Goose Island 02 MN-WI Mississippi 694.7 M694.7L 15 4848046 641197 MC Coney Island 02 MN-WI Mississippi 694.7 M694.7M 15 4848012 641222 MC Coney Island 02 MN-WI Mississippi 696.5 M696.5D 15 4850291 638947 BWC Target Lake 02 MN-WI Mississippi 696.5 M696.5F 15 4850396 639088 BWC Target lake 02 MN-WI Mississippi 696.8 M696.8I 15 4850832 639499 MC Municipal wing dam 02 MN-WI Mississippi 698.1 M698.1G 15 4852776 637410 BWI Blue Lake 02 MN-WI Mississippi 698.3 M698.3D 15 4853101 637038 BWI Blue Lake 02 MN-WI Mississippi 698.5 M698.5B 15 4853457 636664 BWI Blue Lake 02 MN-WI Mississippi 700.2 M700.2F 15 4855029 638502 SC East Channel 0
B-5

Table B-1. Continued.

Field

station State River name

River mile

Location codea

UTM zone Northing Easting

Habitat classb Additional comments

Fs

2 MN-WI Mississippi 701 M701.0B 15 4856320 637025 MC Main Channel 02 MN-WI Mississippi 701.1 M701.1B 15 4856266 637184 MC east side of main channel transect 02 MN-WI Mississippi 701.1 M701.1C 15 4856345 637101 MC high flow only transect site 02 MN-WI Mississippi 701.1 M701.1D 15 4856345 637028 MC transect site-mid channel 02 MN-WI Mississippi 701.1 M701.1E 15 4856345 636956 MC high flow only transect site 02 MN-WI Mississippi 701.1 M701.1F 15 4856345 636883 MC transect site-west side 02 MN-WI Mississippi 701.4 M701.4I 15 4856771 639027 BWC French Lake 12 MN-WI Mississippi 701.7 M701.7I 15 4856771 639027 BWC French Lake 02 MN-WI Mississippi 701.8 M701.8C 15 4857532 639936 BWC East Channel 02 MN-WI Mississippi 701.8 M701.8H 15 4857032 638944 BWC fisheries site 12 MN-WI Mississippi 702.3 M702.3A 15 4857754 635988 MC MN side upstream of landing 02 MN-WI Mississippi 702.7 M702.7T 15 4858536 637731 IMP French Island Spillway 02 MN Root 0.1 R000.1M 15 4846727 640647 TRIB mid-stream enters pool 8 RM 693.6 02 IA Upper Iowa 2.9 UI02.9M 15 4814694 637926 TRIB mid-stream HWY 26 bridge enters 

pool 9 near RM 671

0

3 IL Apple 2.3 AL02.3M 15 4674120 728180 TRIB mid-stream Army Depot Rd west of 

HWY 84

0

3 IA CatFish 

Creek

0.3 CF00.3M 15 4704017 693417 TRIB mid-stream in Mines of Spain state 

park

0

3 IA Elk 2.4 ER02.4M 15 4652639 732645 TRIB mid-stream HWY 67 bridge 03 IL Galena 3.6 GA03.6M 15 4698150 711420 TRIB mid-stream off RR bridge S edge of 

town

1

3 IA-IL Mississippi 497.2 M497.2B 15 4608462 721528 MC LeClaire 03 IA-IL Mississippi 508.1 M508.1F 15 4626096 723487 BWC Shricker’s Slough 03 IA-IL Mississippi 511.4 M511.4B 15 4628610 728030 MC Camanche 03 IA-IL Mississippi 520.6 M520.6B 15 4639310 734615 MC Clinton 03 IA-IL Mississippi 524.2 M524.2X 15 4644447 738835 BWC boat ramp at Mickelson’s Landing 03 IA-IL Mississippi 525.3 M525.3I 15 4646547 735895 IMP lower Pool 13 03 IA-IL Mississippi 525.5 M525.5C 15 4645596 733769 IMP transect site west side 03 IA-IL Mississippi 525.5 M525.5F 15 4645539 734965 IMP transect site west side 0
B-6

Table B-1. Continued.

Field

station State River name

River mile

Location codea

UTM zone Northing Easting

Habitat classb Additional comments

Fs

3 IA-IL Mississippi 525.5 M525.5J 15 4647031 735977 IMP transect site mid-channel 03 IA-IL Mississippi 525.5 M525.5K 15 4646192 736250 IMP transect site mid-channel 03 IA-IL Mississippi 525.5 M525.5L 15 4646920 735830 IMP Impounded area east of main channel 

- fixed site

0

3 IA-IL Mississippi 525.5 M525.5N 15 4647293 736505 IMP transect site east side 03 IA-IL Mississippi 525.8 M525.8H 15 4647203 735591 IMP lower Pool 13 03 IA-IL Mississippi 526 M526.0G 15 4647326 735800 IMP lower Pool 13 03 IA-IL Mississippi 529.7 M529.7L 15 4652726 736832 MC near Smith Bay light and daymark 03 IA-IL Mississippi 529.7 M529.7M 15 4652779 737208 MC near Smith Bay light and daymark 

east channel border

0

3 IA-IL Mississippi 530.2 M530.2K 15 4653724 736618 MC east channel border belown wing dam 03 IA-IL Mississippi 530.3 M530.3K 15 4653780 736622 MC east channel border on wing dam 03 IA-IL Mississippi 530.9 M530.9G 15 4654588 735786 BWC in Elk Wildlife Refuge 03 IA-IL Mississippi 532.2 M532.2T 15 4656988 737891 BWC Spring Lake 03 IA-IL Mississippi 532.3 M532.3T 15 4656988 737891 BWC Spring Lake Fixed Site 03 IA-IL Mississippi 534.8 M534.8L 15 4660508 734751 BWC lower end of Edick Lake 03 IA-IL Mississippi 535.9 M535.9J 15 4662145 733189 BWC lower end of Town Lake 03 IA-IL Mississippi 535.9 M535.9K 15 4662054 733511 SC lower end of Running Slough 03 IA-IL Mississippi 536.2 M536.2P 15 4663472 734166 SC Eldridge Slough 03 IA-IL Mississippi 536.4 M536.4B 15 4662625 732416 BWC Barge Lake 03 IA-IL Mississippi 536.8 M536.8L 15 4663476 733596 BWC upper end of Eldridge Slough 03 IA-IL Mississippi 536.9 M536.9M 15 4663573 733888 BWC upper end of Eldridge Slough 03 IA-IL Mississippi 540.2 M540.2T 15 4668352 733781 BWC Savanna Bay fixed site 03 IA-IL Mississippi 541.7 M541.7L 15 4668876 731882 BWC upper end of Savanna Bay 03 IA-IL Mississippi 542.5 M542.5E 15 4669388 729999 BWC Lower end of Pinoak Lake 03 IA-IL Mississippi 542.7 M542.7C 15 4669270 729830 MC Lower end of Pinoak Lake 13 IA-IL Mississippi 543.2 M543.2L 15 4670688 730102 MC channel border near Big Soupbone 

Island

0

3 IA-IL Mississippi 543.2 M543.2M 15 4670786 730189 MC channel border near Big Soupbone 

Island

0

3 IA-IL Mississippi 543.6 M543.6G 15 4670128 728972 BWC Upper end of Pinoak Lake 0
B-7

Table B-1. Continued.

Field

station State River name

River mile

Location codea

UTM zone Northing Easting

Habitat classb Additional comments

Fs

3 IA-IL Mississippi 544.1 M544.1D 15 4669899 728204 BWC upper end of Lainsville Slough 03 IA-IL Mississippi 544.2 M544.2C 15 4669840 728063 BWC dredge cut near entrance to Lower 

Brown’s Lake

0

3 IA-IL Mississippi 544.2 M544.2D 15 4669884 728068 BWC edge of dredge cut near entrance to 

Lower Brown’s Lake

0

3 IA-IL Mississippi 544.5 M544.5F 15 4670287 727615 BWC deep dredge hole in Lower Brown’s 

Lake dredge cut

0

3 IA-IL Mississippi 544.6 M544.6E 15 4670292 727301 BWC Lower Brown’s Lake dredge cut 03 IA-IL Mississippi 544.6 M544.6F 15 4670419 727542 BWC Lower Brown’s Lake dredge cut 03 IA-IL Mississippi 544.7 M544.7F 15 4670569 727508 BWC edge of Lower Brown’s Lake dredge 

cut

0

3 IA-IL Mississippi 545.1 M545.1H 15 4670776 726951 BWC Dredge hole in Scarborough portion 

of Brown’s Lake complex

0

3 IA-IL Mississippi 545.5 M545.5B 15 4670292 726317 BWC Upper Brown’s Lake dredge cut fixed 

site

0

3 IA-IL Mississippi 545.5 M545.5C 15 4670307 726350 BWC Upper Brown’s Lake dredge cut 03 IA-IL Mississippi 545.8 M545.8F 15 4670793 726102 MC cut from Brown’s Lake inlet structure 

into Upper Brown’s Lake

0

3 IA-IL Mississippi 546.5 M546.5L 15 4672479 725249 MC channel border near Maquoketa Levee 

Light and Daymark

0

3 IA-IL Mississippi 546.7 M546.7P 15 4673328 725255 BWC N of Maquoketa Levee Light and 

Daymark

0

3 IA-IL Mississippi 550.4 M550.4L 15 4675310 719859 MC west side of channel below wing dam 03 IA-IL Mississippi 550.5 M550.5L 15 4675321 719815 MC west side of channel on wing dam 03 IA-IL Mississippi 551.3 M551.3M 15 4676806 719234 BWC lower end of Crooked Slough 03 IA-IL Mississippi 551.3 M551.3N 15 4676895 719457 BWC lower end of Crooked Slough 03 IA-IL Mississippi 551.6 M551.6N 15 4677202 718446 BWC lower end of Crooked Slough 03 IA-IL Mississippi 552.3 M552.3L 15 4676383 717210 MC main channel north of Island 254 

Light & Daymark

1

3 IA-IL Mississippi 554 M554.0G 15 4678142 715730 SC side channel downstream of Bellevue 

Lower Light & Daymark

0
B-8

Table B-1. Continued.

Field

station State River name

River mile

Location codea

UTM zone Northing Easting

Habitat classb Additional comments 

3 IA-IL Mississippi 554.2 M554.2C 15 4678085 714831 MC lower end of Harrington Slough 3 IA-IL Mississippi 554.3 M554.3C 15 4678229 714718 MC lower end of Harrington Slough 3 IA-IL Mississippi 554.3 M554.3D 15 4678161 714925 MC lower end of Harrington Slough 3 IA-IL Mississippi 554.8 M554.8E 15 4678589 714227 MC channel site just west of Bellevue 

Lower Light and Daymark

3 IA-IL Mississippi 554.8 M554.8F 15 4679382 714669 MC At Bellevue Lower Light & Daymark channel border 3 IA-IL Mississippi 556 M556.0E 15 4680920 713388 MC mid-stream near mouth of Mill Cr. 3 IA-IL Mississippi 556.4 M556.4A 15 4681070 712780 MC L and D 12 tailwater 3 IA-IL Mississippi 556.4 M556.4C 15 4681712 712828 MC tailwater west side 3 IA-IL Mississippi 556.6 M556.6E 15 4681712 712960 MC tailwater mid-stream 3 IA-IL Mississippi 563.9 M563.9T 15 4692590 711305 BWC Sunfish Lake 3 IA-IL Mississippi 564.5 M564.5T 15 4693461 710457 BWC upper end of Sunfish Lake 3 IA-IL Mississippi 566.2 M566.2R 15 4695192 708476 BWC just west of Harris Slough 3 IA-IL Mississippi 574.2 M574.2D 15 4701302 698355 SC side channel behind Nine Mile 

Island

3 IA-WI Mississippi 582.5 M582.5B 15 4711424 693500 MC L and D 11 tailwater 3 IA-WI Mississippi 615.2 M615.2B 15 4738150 655880 MC L and D 10 tailwater Guttenberg 3 IA Mill Creek 1 MC01.0M 15 4680820 711480 TRIB West side of Bellevue 3 IA Maquoketa 0.1 MQ00.1M 15 4673779 722089 TRIB at confluence with Mississippi R 3 IA Maquoketa 2.1 MQ02.1M 15 4671190 720130 TRIB mid-stream HWY 52 bridge 3 IL Plum 3.2 PR03.2M 15 4662123 737762 TRIB mid-stream HWY 84 bridge 3 IL Rush Creek 1.7 RC01.7M 15 4671160 732650 TRIB mid-stream HWY 84 bridge 3 IA Rock Creek 0.1 RK00.1M 15 4628602 725088 TRIB mid-stream HWY 67 bridge 3 IA Rock Creek 3.7 RK03.7M 15 4630693 723012 TRIB mid-stream 3 IA Turkey 4.8 TK04.8M 15 4729939 657604 TRIB mid-stream HWY 52 bridge 3 IA Tete de Mortes 

Creek

4.1 TM04.1M 15 4692280 703053 TRIB mid-stream HWY 52 bridge 

3 IA Wapsipinicon 2.6 WP02.6M 15 4622695 719618 TRIB mid-stream HWY 67 bridge 4 MO Bob’s Creek 4.6 BC04.6M 15 4315141 695569 TRIB mid-stream 
B-9

Table B-1. Continued.

Field

station State River name

River mile

Location codea

UTM zone Northing Easting

Habitat classb Additional comments 

4 IL Cahokia Creek 0.4 CA00.4M 15 4298975 751328 TRIB below spillway on S side of creek 4 MO Cuivre 11.6 CU11.6M 15 4310565 695163 TRIB mid-stream HWY 79 bridge 4 MO Dardenne 

Creek

1 DC01.0M 15 4303092 712694 TRIB mid-stream HWY B bridge 

4 IL Illinois 0 I000.0V 15 4316002 719584 MC confluence mix 4 IL Illinois 2 I002.0Y 15 4316012 719428 MC confluence Illinois 4 IL Illinois 5.7 I005.7M 15 4313347 714703 BWC lower Swan Lake near mouth 4 IL Illinois 5.8 I005.8K 15 4313556 714649 BWC lower Swan Lake 4 IL Illinois 7 I007.0W 15 4315756 712523 MC Pere Marquette State Park 4 MO-IL Mississippi 193.2 M193.2F 15 4297372 748748 MC transect- MO side 4 MO-IL Mississippi 193.2 M193.2H 15 4297202 748922 MC transect - mid-stream 4 MO-IL Mississippi 193.2 M193.2J 15 4296989 749100 MC transect - IL side 4 MO-IL Mississippi 196.9 M196.9Q 15 4302053 750631 MC across from Shell Plant 4 MO-IL Mississippi 201.7 M201.7Q 15 4305854 744970 IMP-L Ellis Bay open water 4 MO-IL Mississippi 202.2 M202.2N 15 4306157 743830 IMP-L Ellis Bay shore 4 MO-IL Mississippi 202.2 M202.2R 15 4306204 744769 IMP-L Alton Slough 4 MO-IL Mississippi 202.2 M202.2V 15 4306563 744990 IMP channel border 4 MO-IL Mississippi 202.6 M202.6T 15 4307283 744053 MC transect site 4 MO-IL Mississippi 202.6 M202.6V 15 4307404 744476 MC transect site 4 MO-IL Mississippi 202.6 M202.6X 15 4307404 744838 MC transect site 4 MO-IL Mississippi 202.9 M202.9N 15 4306696 743418 BWI Ellis Lake 4 MO-IL Mississippi 202.9 M202.9Q 15 4306774 743661 BWI Ellis Lake 4 MO-IL Mississippi 203.5 M203.5Q 15 4307244 742887 IMP West Alton Bay 4 MO-IL Mississippi 203.5 M203.5R 15 4307339 742896 IMP West Alton Bay 4 MO-IL Mississippi 205.8 M205.8K 15 4308992 739745 BWI Spatterdock Lake 4 MO-IL Mississippi 206 M206.0S 15 4309158 739884 BWC Brickhouse Slough 4 MO-IL Mississippi 206.1 M206.1T 15 4309408 739967 BWI Dresser Island 4 MO-IL Mississippi 207.9 M207.9Q 15 4309780 737332 MC Brickhouse Slough (levee on site 

now)

4 MO-IL Mississippi 211.2 M211.2P 15 4311972 731978 MC Portage 
B-10

Table B-1. Continued.

Field

station State River name

River mile

Location codec

UTM zone Northing Easting

Habitat classb Additional comments

4 MO-IL Mississippi 212.3 M212.3X 15 4313163 731133 MC Portage wing dam 4 MO-IL Mississippi 212.4 M212.4X 15 4313146 731177 MC Portage wing dam 4 MO-IL Mississippi 219.4 M219.4U 15 4315208 720533 MC Mason Island wing dam 4 MO-IL Mississippi 219.5 M219.5U 15 4315191 720522 MC Mason Island wing dam eddy 4 MO-IL Mississippi 220.2 M220.2T 15 4315993 719428 SC confluence Mississippi 4 MO-IL Mississippi 224.2 M224.2S 15 4308859 716523 SC Bolter Island 4 MO-IL Mississippi 235.3 M235.3D 15 4309963 702654 BWI Bernard Lake 4 MO-IL Mississippi 235.5 M235.5D 15 4310285 702472 BWI Bernard Lake 4 MO-IL Mississippi 235.6 M235.6J 15 4310861 702973 MC Hat Island 4 MO-IL Mississippi 237.2 M237.2G 15 4312554 701683 BWC Turkey Island Slough 4 MO-IL Mississippi 237.3 M237.3T 15 4313769 701581 MC Turkey Island wing dam 4 MO-IL Mississippi 237.4 M237.4T 15 4313786 701569 MC Turkey Island wing dam 4 MO-IL Mississippi 240.9 M240.9M 15 4319612 700657 MC Lock and Dam 25 Tailwater 4 MO-IL Mississippi 241.3 M241.3K 15 4319635 700638 MC Lock and Dam 25 Tailwater 4 MO-IL Mississippi 241.4 M241.4K 15 4319647 700637 MC Lock and Dam 25 Tailwater wing 

dam

4 MO Missouri 2 MO02.0X 15 4301655 748277 TRIB Missouri 4 MO Peruque Creek 1.8 PE01.8M 15 4306271 703159 TRIB mid-stream 4 IL Piasa Creek 0.2 PI00.2M 15 4313310 735030 TRIB mid-stream 4 IL Wood 0.2 WD00.2M 15 4305319 749105 TRIB between Rte. 143 bridge and 

spillway

5 IL Big Muddy 0.7 BM00.7S 15 4164557 808267 TRIB South bank 5 IL Cache 1.1 CR01.1M 15 4112433 832994 TRIB Mid channel 5 MO Headwaters 

Diversion

0.5 HD00.5M 16 4125220 276500 TRIB formerly Little R. 

5 MO Headwaters 

Diversion

0.9 HD00.9M 15 4127458 808024 TRIB formerly Little R. 
B-11

Table B-1. Continued.

Field

station State River name

River mile

Location codea

UTM zone Northing Easting

Habitat classb Additional comments F

5 MO-IL Mississippi 9.7 M009.7M 15 4106471 834768 MC Natural bank 5 MO-IL Mississippi 28.8 M028.8K 15 4104444 823740 MC Bumgard side channel 5 MO-IL Mississippi 30.5 M030.5J 15 4106136 822390 SC Bumgard side channel 5 MO-IL Mississippi 30.9 M030.9M 15 4107252 821148 MC MO bank 5 MO-IL Mississippi 32.2 M032.2M 15 4108748 821631 MC MO bank 5 MO-IL Mississippi 33.7 M033.7M 15 4110878 821525 MC MO bank 5 MO-IL Mississippi 34.2 M034.2M 15 4111566 821114 BWC Santa Fe Side channel on MO bank 5 MO-IL Mississippi 35.7 M035.7O 15 4114510 820513 SC Santa Fe side channel 5 MO-IL Mississippi 38 M038.0N 15 4118249 817577 BWC Santa Fe side channel 5 MO-IL Mississippi 38.1 M038.1J 15 4116525 817510 MC revetted channel border above wing 

dam

5 MO-IL Mississippi 38.5 M038.5J 15 4116894 817366 MC revetted channel border above wing 

dam

5 MO-IL Mississippi 38.5 M038.5N 15 4117455 818189 SC Santa Fe Side channel 5 MO-IL Mississippi 39.2 M039.2N 15 4118384 817415 BWC revetted channel border 5 MO-IL Mississippi 41.1 M041.1L 15 4120242 815692 MC Unstructured natural bank 5 MO-IL Mississippi 48 M048.0O 15 4128917 810930 SC Marquette side channel lower 5 MO-IL Mississippi 48.4 M048.4M 15 4128447 810505 MC Lower Inside bend of Marquette 

island

5 MO-IL Mississippi 48.5 M048.5M 15 4129592 810192 BWC Cape Bend 5 MO-IL Mississippi 48.9 M048.9G 15 4128578 809146 MC Cape bend 5 MO-IL Mississippi 50.7 M050.7I 15 4131395 809127 SC Upper Marquette side channel 5 MO-IL Mississippi 50.8 M050.8I 15 4131500 809039 BWC Upper Marquette side channel 5 MO-IL Mississippi 53.8 M053.8B 15 4136480 811240 MC Main channel border revetted bank 5 MO-IL Mississippi 54.2 M054.2B 15 4136988 811140 MC Mid channel below Picayune outlet 5 MO-IL Mississippi 55.9 M055.9D 15 4137754 813107 MC channel border below wing dike 5 MO-IL Mississippi 56 M056.0I 15 4136456 813140 SC Lower Picayune side channel 5 MO-IL Mississippi 57.9 M057.9L 15 4138345 816587 SC Picayune side channel near hardpoint 5 MO-IL Mississippi 59.2 M059.2D 15 4141154 815774 BWC Picayune side channel 
B-12

Table B-1. Continued.

Field

station State River name

River mile

Location codea

UTM zone Northing Easting

Habitat classb Additional comments

Fs

5 MO-IL Mississippi 59.5 M059.5I 15 4140542 817387 SC Upper Picayune side channel 05 MO-IL Mississippi 60.3 M060.3D 15 4142292 815843 SC Schinemann chute 200m above 

closing structure

0

5 MO-IL Mississippi 61.2 M061.2C 15 4143708 816659 MC Main channel border 05 MO-IL Mississippi 62 M062.0B 15 4144942 816178 SC top of Schinemann chute 05 MO-IL Mississippi 66.3 M066.3A 15 4150536 813525 MC Main channel border at Trail of 

Tears transect site

0

5 MO-IL Mississippi 66.3 M066.3B 15 4151068 813325 MC Mid channel at Trail of Tears 

transect site

0

5 MO-IL Mississippi 66.4 M066.4C 15 4151106 813883 MC Main channel border at Trail of 

Tears transect site

0

5 MO-IL Mississippi 69.4 M069.4C 15 4154920 810662 MC channel border above wing dam 05 MO-IL Mississippi 70.1 M070.1C 15 4155779 810256 MC Main channel border at Neely’s 

landing

0

5 MO-IL Mississippi 70.2 M070.2A 15 4155709 809550 MC Main channel border at Neely’s 

landing

0

5 MO-IL Mississippi 70.4 M070.4C 15 4156188 810125 MC Main channel border at Neely’s 

landing

0

5 MO-IL Mississippi 75.1 M075.1C 15 4163004 807489 MC channel border below wing dam 05 MO-IL Mississippi 76.2 M076.2C 15 4164635 807529 MC channel border above wing dam 05 MO-IL Mississippi 77.9 M077.9A 15 4167389 807337 SC Cottonwood side channel near MO 

bank

0

5 MO-IL Mississippi 78 M078.0B 15 4167464 807933 MC Outside buoy line on the inside 

bend of Cottonwood island

0

5 MO-IL Mississippi 79.3 M079.3B 15 4168704 808215 MC Rock piles above cottonwood 

island

0

6 IL Illinois 80.2 I080.2C 15 4423724 710613 MC LaGrange L/D near dam wall 06 IL Illinois 80.2 I080.2M 15 4423711 710757 MC LaGrange L/D mid channel 06 IL Illinois 94.8 I094.8D 15 4441126 722694 SC . 06 IL Illinois 95.2 I095.2C 15 4441535 722628 MC . 06 IL Illinois 98 I098.0C 15 4444200 725466 BWC . 06 IL Illinois 99.4 I099.4C 15 4445489 727389 BWC . 0
B-13

Table B-1. Continued.

Field

station State River name

River mile

Location codea

UTM zone Northing Easting

Habitat classb Additional comments Fir

6 IL Illinois 99.4 I099.4D 15 445436 727389 BWC . 096 IL Illinois 106.5 I106.5X 15 4447352 739042 BWC . 096 IL Illinois 106.5 I106.5Y 15 4447313 739082 BWC . 096 IL Illinois 106.8 I106.8X 15 4447933 739451 BWC . 106 IL Illinois 107 I107.0S 15 4448554 738347 SC . 096 IL Illinois 107.2 I107.2R 15 4448885 738242 MC . 096 IL Illinois 109.5 I109.5D 15 4453509 738629 BWI Anderson Lake 1/2 mi out ramp 096 IL Illinois 113 I113.0T 15 4455335 743376 SC east side of Bath Chute 096 IL Illinois 121.2 I121.2W 15 4466765 749108 MC east side near marker 096 IL Illinois 121.5 I121.5X 15 4466910 749599 SC . 096 IL Illinois 122.5 I122.5X 15 4468394 750637 BWC . 096 IL Illinois 122.6 I122.6Y 15 4468389 750707 BWC west side of Quiver Lake 096 IL Illinois 124.8 I124.8R 15 4471935 751508 BWI . 046 IL Illinois 127.9 I127.9W 15 4473468 755714 BWI . 046 IL Illinois 128.8 I128.8F 15 4474868 755668 SC . 086 IL Illinois 128.8 I128.8T 15 4474258 756326 BWI . 096 IL Illinois 128.8 I128.8W 15 4474253 756813 BWI . 096 IL Illinois 129.8 I129.8W 15 4475007 757518 BWI . 076 IL Illinois 135.8 I135.8W 15 4483187 764092 BWI . 106 IL Illinois 135.8 I135.8X 15 4482995 764206 BWI . 106 IL Illinois 157.8 I157.8D 15 4501489 783249 MC Peoria L/D east rock wall 046 IL LaMoines 0.5 LM00.5M 15 4429191 711723 TRIB middle near mouth 096 IL LaMoines 7.2 LM07.2M 15 4428445 707351 TRIB mid bridge on Lock and Dam Rd 06 IL Mackinaw 4.4 MK04.4M 15 4491575 776765 TRIB mid bridge 1mi off Manito Blacktop 046 IL Quiver Creek 4.6 QV04.6M 15 4468071 758620 TRIB mid bridge 1mi off Manito Blacktop 046 IL Spoon 0.2 S000.2K 15 4465581 748649 TRIB west side near mouth 126 IL Sangamon 16.2 SG16.2C 15 4438599 743373 TRIB mid bridge Hwy 78 047 IA-WI Mississippi 646.9 M646.9X 15 4784632 653383 MC Gordons Bay Landing 09
B-14

HDxx.xM = Headwaters Diversion, Missouri 

(formerly Little River)

Ixxx.xM = Illinois River, IllinoisIWxx.xM = Iowa River, IowaKKxx.xM = Kaskaskia River, IllinoisLMxx.xM = LaMoines River, IllinoisLRxx.xM = Little River, Missouri (replaced 

by HD above)

LXxx.xM = La Crosse River, WisconsinMxxx.xM = Mississippi River (main stem)MCxx.xM = Mill Creek, IowaMKxx.xM = Mackinaw River, IllinoisMOxx.xM = Missouri River, MissouriMQxx.xM = Maquoketa River, IowaPExx.xM = Peruque Creek, MissouriPIxx.xM = Piasa Creek, IllinoisPRxx.xM = Plum River, IllinoisQVxx.xM = Quiver Creek, Illinois

Table B-1. Continued.

Field

station State River name

River mile

Location codea

UTM zone Northing Easting

Habitat classb Additional comments F

7 IA-WI Mississippi 647.9 M647.9X 15 4785905 654366 MC LD 9 at first roller gate 7 IA-WI Mississippi 663.4 M663.4E 15 4803341 645390 MC Big Slough at Lansing bridge 7 IA-WI Mississippi 666.3 M666.3N 15 4806582 644210 BWC Big Lake at Lansing (backwater) 7 IA-WI Mississippi 667.8 M667.8F 15 4808265 641825 BWC Botsford (backwater north of Lansing) 7 WI Wisconsin 5 WS05.0Y 15 4762468 659005 TRIB Highway 18 Bridge 7 IA Yellow 1.5 YL01.5Y 15 4772580 646725 TRIB Effigy Mounds 

aThe following list is the codes for fixed-site sampling locations in the Long Term Resource Monitoring Program. The “xx.x” designation is the distancfrom the confluence of the tributary and the main stem of the Mississippi River (or Illinois River, where applicable). See Sections 1.5.1 and 1.5.2 for fucodes.

APxx.xM = Apple River, MissouriALxx.xM = Apple River, IllinoisBCxx.xM = Bob’s Creek, MissouriBFxx.xM = Buffalo River, WisconsinBKxx.xM = Black River, WisconsinBMxx.xM = Big Muddy River, IllinoisBXxx.xM = Bad Axe River, WisconsinCAxx.xM = Cahokia Creek, IllinoisCFxx.xM = CatFish Creek, IowaCNxx.xM = Cannon River, MinnesotaCCxx.xM = Coon Creek, WisconsinCHxx.xM = Chippewa River, WisconsinCRxx.xM = Cache River, IllinoisCUxx.xM = Cuivre River, MissouriDCxx.xM = Dardenne Creek, MissouriDMxx.xM = Des Moines River, IowaERxx.xM = Elk River, IowaGAxx.xM = Galena River, Illinois

Rxxx.xM = Root River, MinnesotRCxx.xM = Rush Creek, IllinoisRKxx.xM = Rock Creek, IowaSxxx.xM = Spoon River, IllinoisSGxx.xM = Sangamon River, IllinSKxx.xM = Skunk River, IowaSXxx.xM = St. Croix River, MinnTMxx.xM = Tete de Mortes CreekTKxx.xM = Turkey River, IowaUIxx.xM = Upper Iowa River, IowVMxx.xM = Vermillion River, MinWDxx.xM = Wood River, IllinoisWWxx.xM = Whitewater River, MiWPxx.xM = Wapsipinicon River, IWSxx.xM = Wisconsin River, WisYLxx.xM = Yellow River, IowaZMxx.xM = Zumbro River, Minne

bBWC = backwaters, contiguous; BWI = backwaters, isolated; IMP = impounded areas; IMP-L = Pepin or Swan Lake; MC = main channel; SC = side TRIB = tributarycAs of publication date, sampling was planned to resume or continue at these sites in 2004.dThese sites were sampled for a reduced set of variables every 4 weeks from April to December 2003.
C-1

Appendix C. Instrument Performance Quality Factor Codes

 The performance of water quality monitoring instruments in the Long Term Resource Monitoring 

Program is rated on a graduated scale from fully acceptable to nonoperational. A quality factor code 

is assigned to each reading based on performance of the instrument in the field (if noticeably aberrant) 

and on calibration checks at the end of the sampling day (Table C-1).

Table C-1. Criteria for assigning quality factor (QF) codes to instrument readings in Long Term Resource Monitoring Program 

water quality monitoring based on deviations from calibration after sampling (down calibration). A blank QF indicates that 

readings are fully within requirements, 1 indicates acceptable, but slightly degraded performance, D indicates performance 

below acceptable standards, 0 indicates that readings cannot be used, but are recorded for diagnostic purposes and documentation only.

Deviation (+/-) required for quality factor

Parameter Blank “1” “D” “0” (zero)

Dissolved oxygen (mg/L) < 0.24 0.25B0.50 0.51B1.0 >1.0

pH (units) < 0.20 0.21B0.25 0.26B0.30 >0.30

Conductivity (μS) < 14 15B20 21B27 >27

Turbiditya 2% of cal.

standard

3B5% of cal.

standard

6B10% of cal. 

standard

>10% of cal.

standard

 aTurbidity deviations of <1 nephelometric turbidity unit from calibration standard receive a blank QF code.
D-1

Appendix D. Field Instrument Maintenance and Calibration

 In general, maintenance and calibration of 

field instruments in the Long Term Resource 

Monitoring Program (LTRMP) is performed 

according to the manufacturer’s instructions. 

This appendix provides more detailed and 

specific guidelines.

D.1 Acoustic Depth Finder

 Acoustic depth finders should be calibrated 

before first use and any time behavior seems 

questionable or after a major repair or alteration 

has been performed on the device. Some 

nonlinearity has been observed in these devices 

so that conversion to actual depth may not be 

precise. Water temperature can also make a small 

difference in calibration.

 A calibration table or figure should be created 

for each acoustic depth finder in service. The 

measurements needed for this calibration should 

be taken in quiescent water (velocity <2 cm/sec) 

using a calibrated sounding line (such as used 

for Secchi disk transparency measurements). 

The sounding line with acoustic target attached 

is lowered over the side (or transom) and is 

centered as much as possible in the signal cone 

of the depth finder’s transducer. Positioning of 

the crew members and cargo in the boat should 

be arranged to ensure the transducer is pointed 

vertically downward and does not change during 

the calibration process. A clear and distinct 

return signal from the target should be apparent. 

Using at least 5 depths, the reading of the 

instrument and the actual depth to the target are 

recorded. If possible, the maximum depth used 

in this exercise should encompass the maximum 

depth observed in the field. A linear regression of 

the actual depth on instrument reading can then 

be used to correct the acoustic sounder readings 

or verify its performance. Deviation of sounder 

readings from actual depth should be less than 

10%. This check should be performed initially at 

high and low temperature extremes, and then at 

least once per year on each instrument.

D.2 Multiparameter Monitoring Instrument

 Since 1993, LTRMP water quality monitoring 

has used multiparameter monitoring instruments 

(Hydrolab Corporation, Loveland, CO) for 

in situ measurements of water temperature, 

dissolved oxygen, pH, and specific conductance. 

Routine maintenance of these probes is crucial 

to obtaining good quality data; therefore, 

LTRMP multiparameter instruments undergo 

maintenance and cleaning on a monthly basis, or 

as instrument performance and fouling dictate. A 

check list is provided for documentation of the 

monthly maintenance procedures (Appendix J). 

Specific instructions for care, maintenance, and 

calibration of the individual probes on these 

instruments are described in the instrument 

manuals (Hydrolab Corporation 1991a,b, 1997) 

and should be consulted for additional details. 

The instructions provided here augment or 

supplant those given in the instrument manuals. 

D.2.1 Dissolved Oxygen

 The LTRMP has used three calibration 

methods for electrometric dissolved oxygen 

sensors: saturated air and saturated water 

for daily or site-specific calibrations and the 

Winkler Method (azide modification) for 

quarterly calibrations and equipment crosschecks. The Winkler Method has great reliability 

and demonstrated accuracy (i.e., 0.2 mg/L). 

However, it is too time-consuming for frequent 

laboratory or field use and requires the use of 

toxic and hazardous materials (i.e., sodium 

azide). Therefore, saturation methods are used 

for all oxygen meter calibrations in LTRMP. 

The air saturation method can be done on-site 

relatively quickly and with acceptable accuracy 

and precision; it requires atmospheric air that is 

saturated with water vapor. The saturated water 

method is less vulnerable to method errors and is 

preferred over atmospheric air saturation.

 Air or saturated water calibration is conducted 

before and at the end of the sampling day to keep 
D-2

track of daily machine drift. Drift, determined 

from daily down-calibration procedures, is 

tracked on a control chart (Appendix J). If drift 

is outside of acceptible limits, then the data for 

the whole sampling day must be flagged with 

appropriate QF codes (Appendixes C and J). 

In addition, if a nontemperature-compensated 

probe is used (i.e., required for YSI model 57®, 

but not Hydrolab DataSonde3® or Minisonde®), 

then a saturated air calibration should be 

performed at ambient temperature before each 

measurement. The initials of the crew leader on 

the calibration sheet and crew leader code on the 

data sheet provide verification that the dissolved 

oxygen meter was calibrated according to these 

instructions.

 Dissolved oxygen meter calibration must 

be checked quarterly using an air-saturated 

water bath. The zero point of the instrument is 

also checked quarterly using a sodium sulfite 

solution with cobalt chloride catalyst. When 

oxygen concentrations <1 mg/L are encountered 

or anticipated in the field, the zero point of the 

instrument must be checked on that sampling 

day. All the intermediate results (i.e., date, 

temperature, barometric pressure, calculated 

saturation value) are recorded on the quarterly 

dissolved oxygen calibration and performance 

sheet (Appendix J).

D.2.1.1 Calibration with Saturated Air or Water

a. If using saturated water for calibration, 

aeration of low-ionic-strength (i.e., 

deionized) water should be started at least 

1–2 hours before calibration.

b. Follow the daily check-out and maintenance 

guidelines for the instrument, such as battery 

charge, membrane condition, and meter 

function, to prepare it for use.

c. Allow the instrument to warm up as required 

by the manufacturer’s instructions.

d. Place the probe in the calibration chamber. If 

the probe itself is immersed in the standard, 

use low-ionic-strength water (<500 μS) to 

avoid any interference because of salinity or 

salinity corrections. Tap water may suffice; 

but deionized (DI) water is often necessary. 

e. Turn the instrument on and monitor 

the temperature and dissolved oxygen 

readings in the calibration chamber or 

tank. If appropriate, ensure that the salinity 

correction is disabled. The probe, water, and 

air must all be in thermal equilibrium (same 

temperature) and the calibration media (air or 

water) must be at oxygen saturation. 

f. Obtain the atmospheric pressure (sea-levelcorrected) by calling the nearest weather 

station or referring to a calibrated barometer. 

Local pressure changes associated with 

weather systems can have the same effect 

as moving up or down in altitude more than 

1,000 ft (300 m). Use Table D-1 (assumes 

standard lapse rate of 1.07 inches of Hg/

1,000 ft or 27.18 mm of Hg/1,000 ft) to 

convert the barometric pressure obtained 

from the weather service into absolute 

pressure (standard pressure at sea level 

is 760 mm of Hg). For example, local 

barometric pressure at Cape Girardeau is 

reported as 30.21 inches or 767 mm of Hg (to 

convert from inches to millimeters, multiply 

by 25.4). The absolute pressure needed 

to calculate oxygen solubility is therefore 

767 – 11 = 756 mm of Hg. Using the YSI 

table (Yellow Springs Instrument Company, 

Inc., Yellow Springs, OH), this equates to a 

correction factor of about 0.99.

g. Obtain the temperature of the calibration 

media.

Table D-1. Standard barometric pressure correction for altitude.

Site

Altitude

(ft)

Correction

(mm)

Standard 

pressure

(mm)

Lake City 750 -20 740

Onalaska 700 -19 741

Bellevue 650 -18 742

Great Rivers 420 -12 748

Cape Girardeau 400 -11 749

Havana 430 -12 748
D-3

h. If using a table look-up method, find the 

proper temperature and pressure or pressure 

correction factor on the chart and determine 

the air-saturated value for dissolved oxygen.

i. Adjust meter to read saturated oxygen 

concentration. If the Winkler Method crosscheck is not required, skip steps j and k 

below and record all intermediate results on 

the calibration sheet (Appendix J).

j. Perform a triplicate determination of oxygen 

concentration in the saturated container 

using the Winkler Method (see above). All 

replicates should be within 0.1 mg/L of their 

mean value. Discard and repeat any errant 

determinations. Resolve any discrepancy 

between the triplicate Winkler Method 

results and the calculated saturation value 

(perform additional Winkler determinations 

if necessary). Adjust the meter to read proper 

concentration.

k. Perform a zero point check using a sodium 

sulfite solution as described below. Record 

all intermediate results on the calibration 

sheet (Appendix J).

D.2.1.2 Zero-Point Determination using Sodium 

Sulfite

 Sulfite (SO3) ions will react with dissolved 

oxygen in the presence of trace amounts of cobalt 

ion (catalyst) to form an anoxic solution. This 

solution can be used to check the zero oxygen 

setting of the dissolved oxygen meter. Because 

sulfite is a strong reducing agent, it can interfere 

with Winkler determinations by reducing iodine 

to iodide (result will be lower than actual value) 

and so should not be used to check the zero point 

of a Winkler determination. The zero point of 

most electrometric oxygen meters is quite stable 

and needs to be checked infrequently (monthly). 

However, whenever near-zero oxygen readings 

are anticipated in the field, the meter should be 

checked in this range.

 The method for preparing and using a sulfite 

solution for zero point checking is as follows:

 Use DI water. To a suitable volume (200–

500 mL) of water, add a small amount (about 

100 mg or one quarter teaspoon) of sodium 

sulfite (a few crystals may remain undissolved 

at the bottom of the container). Next add two 

drops of cobalt catalyst (0.001 M solution of 

cobalt chloride). The oxygen concentration 

in the solution will rapidly drop toward zero. 

Submerge the oxygen probe in the solution (use 

a calibration cup if appropriate). Avoid agitation 

and after immersing the sensor, seal the solution 

and sensor off from the air if possible. Within 

2 min, the oxygen meter should register 0.0 mg/L 

of oxygen. If the meter does not register between 

0.0 and 0.2 mg/L, or if the reading is not stable, 

proceed with additional maintenance or repair 

as specified in the instrument manual. Once the 

check is complete, rinse the sensor thoroughly 

under tap water to remove any trace of the anoxic 

test solution. Now repeat the measurement of 

air saturation with DI water (bucket or exposed 

membrane method). The meter reading should 

return to the saturated value within 2 min.

D.2.2 Dissolved Oxygen Electrode Cleaning

 The silver and silver chloride electrode used 

in the dissolved oxygen probe requires occasional 

cleaning. This is indicated by loss of linearity 

(instrument calibrated at one concentration does 

not read correctly at another) or readings that are 

consistently high- or off-scale. The procedure is 

as follows:

 a. Remove the dissolved oxygen membrane 

and discard the electrolyte.

 b. Fill a syringe with 10% ammonium 

hydroxide solution.

 c. Carefully fill the dissolved oxygen cell 

with ammonium hydroxide, using caution 

to keep the ammonium hydroxide solution 

from contacting the gold cathode.

 d. Allow the solution to remain in the sensor 

cell for 10–15 min.

 e. Remove the ammonium hydroxide 

carefully from the sensor cell; use the 

syringe to draw the solution back out or 

use a quick turning motion to eject the 

solution from the cell without it contacting 

the gold cathode.

 f. Rinse the sensor cell thoroughly with 

reagent grade water—repeat at least three 

times. After the first rinse, allow the cell 
D-4

to overflow with rinse water during the 

rinsing process.

 g. Refill the dissolved oxygen sensor cell 

with reference electrolyte and replace the 

membrane.

 h. Allow the membrane to stabilize (relax) for 

at least 8 hours (preferably overnight) after 

replacement. Calibrate instrument before 

use.

D.2.3 Temperature

 Calibration of the temperature probe is 

checked quarterly by comparison to a traceable 

thermometer and to other units in use in the 

LTRMP. Results of this cross-check are held at 

each field station.

D.2.4 pH

 Several factors must be considered in 

calibrating and using a glass membrane pH 

probe:

 a. The pH is Temperature Dependent. The 

actual pH of a calibration buffer varies 

with temperature. This is described in 

a table that usually accompanies the 

buffer container. For example, at 5°C, a 

pH 10 buffer has an actual pH of 10.26. 

In general, calibration buffers and the 

pH probe should be stored at the same 

temperature (20–25°C). In any event, the 

probe and the sample (or buffer) must 

reach thermal equilibrium before an 

accurate reading can be made. There is no 

need to refrigerate buffer solutions; and if 

this is done, it complicates and degrades 

the calibration process. When checking for 

drift in the instrument’s calibration (e.g., in 

measure mode), the actual temperature and 

pH of the buffer must be considered. No 

meter used by the LTRMP can perform this 

check automatically.

 b. Under Field Conditions, Acceptable 

pH Precision is ±0.2. Standard buffers 

have a precision of ±0.02 pH units and 

most field-grade probes and conditions 

allow a precision of about 0.10 pH units. 

Therefore, pH readings outside of ±0.2 are 

unacceptable (±0.10 or better is desirable) 

for LTRMP water quality monitoring. 

 c. The Response of pH Probes is Slower at 

Low Temperatures. Low temperature and 

the presence of interfering materials (i.e., 

phosphate and colloidal clays that clog the 

pores on the glass membrane) can greatly 

slow the response of the probe. Little can 

be done about the temperature effect except 

to allow longer times for equilibration, but 

regular cleaning in dilute hydrochloric acid 

and nondamaging solvents (e.g., alcohol) 

can help with the clogging. Samples 

cannot be warmed to room temperature to 

accelerate the pH measurements (see item 

a above).

D.2.4.1 Daily Calibration

 A glass-membrane pH meter requires 

frequent calibration and maintenance. The 

glass membrane in the measurement electrode 

is extremely delicate and subject to chemical 

and biological fouling and breakage. The 

pH reference electrode is vulnerable to 

contamination and is sensitive to pressure (depth) 

effects.

 Calibration and maintenance procedures 

can vary significantly among models and must 

be performed in strict conformance with the 

operator’s manual for the specific model being 

used (Hydrolab 1991a,b, 1997).

 Calibration of the pH sensor is performed 

by first setting the zero point (pH 7) and then 

setting the slope using a buffer with pH 4 or 10. 

In the LTRMP, the pH 10 buffer is more suitable 

for slope calibration because it represents the 

range more likely to be encountered in the field. 

A back-check to pH 7.0 after setting the slope 

is highly recommended. Drift, determined from 

daily down-calibration procedures, is tracked 

on a control chart (Appendix J). If drift is out 

of acceptable limits, then the data for the whole 

sampling day must be flagged with appropriate 

QF codes (Appendixes C and J). If the pH 

sensor will not calibrate or shows excessive drift 

outside the performance criteria for pH meters, 

it should be serviced or replaced in accordance 
D-5

with the manufacturer’s instructions (Hydrolab 

Corporation 1991a,b, 1997).

D.2.5 Conductivity

 Conductivity is calibrated each day at the 

start and end of sampling and as indicated by 

unusual instrument performance. At least two 

standard solutions are used and procedures 

follow the manufacturer’s instructions (Hydrolab 

Corporation 1991a,b, 1997). Drift, determined 

from daily down-calibration procedures, is 

tracked on a control chart (Appendix J). If drift 

is out of acceptable limits, then the data for 

the whole sampling day must be flagged with 

appropriate QF codes (Appendixes C and J).

 Instruments used for conductivity 

measurements in LTRMP water quality 

monitoring must meet or exceed the following 

requirements:

 a. The device must have a maximum error 

not more than 1% or 1 μS/cm, whichever is 

greater (APHA 1992).

 b. The device meets all of the response 

and sensitivity criteria published by the 

manufacturer.

 c. Criteria 1 and 2 above are checked and met 

for each sampling day.

 d. The equipment automatically compensates 

for temperature and displays specific 

conductance at 25°C.

D.3 Nephelometer 

 Maintenance and calibration requirements 

differ among types of nephelometers. However, 

nephelometers in general require frequent 

calibration and maintenance (e.g., both daily and 

monthly).

 Nephelometer cuvettes should be rinsed with 

distilled water after each day’s use and washed 

with mild soap once a week. A final rinse with 

distilled water is recommended to avoid water 

spots. For in situ instruments (i.e., Hydrolab 

DataSonde3®), the probe should be rinsed with 

mild soapy water at the end of each sampling 

day. Instruments taken into the field must be 

protected from excessive vibration or jarring 

(keep in padded container while in transit); 

in cold weather, instruments must be kept 

above freezing. This can be accomplished by 

keeping the instrument in an insulated container 

(e.g., a cooler) or provided with a heat source 

(Appendix G).

D.3.1 Daily Checklist

a. Check battery or power supply as applicable. 

b. Perform a daily calibration—check against 

three Gelex standards and record in the daily 

calibration control chart (Appendix J).

c. If the calibration is out of acceptable limits 

as indicated on the calibration control 

chart, then the meter must be recalibrated 

with formazin or Hach StablCal® standards 

according to procedures in the following 

section. If the meter is not recalibrated, then 

the appropriate QF codes must be assigned 

(Appendixes C and J). 

D.3.2 Calibration of Hach 2100P with Hach 

StablCal® Stabilized Formazin Standards

 Instructions are provided here for calibration 

of the Hach 2100P meter with Hach StablCal®

Stabilized Formazin Standards because they are 

safer and more convenient to use than manually 

prepared formazin. However, these procedures 

may optionally be used with formazin prepared 

according to instructions in Section F.2.3.4. If 

you are preparing your own standards, then once 

the necessary standards are ready, proceed with 

step “e.”

 a. The StablCal® standards are good for 

24 months from the date of manufacture. 

This ensures 12 months of use. For longterm storage (more than 1 month between 

use), refrigerate at 5°C. Store away from 

direct sunlight. Vials should be stored in 

their original kit with the cover on.

 b. Always allow the standards to acclimate to 

ambient instrument temperature before use 

(not to exceed 40°C).

 c. Shake the 20-, 100-, and 800-NTU 

StablCal® standards vigorously for 2–3 

min if they have been sitting for more than 

1 week. DO NOT SHAKE OR INVERT 
D-6

the <0.1-NTU standard. Let standards sit 

undisturbed for 5 min.

 d. Invert StablCal® standards two to three 

times (except <0.1 NTU) and let sit 2–3 

min. Oil and wipe outside of StablCal®

standards, read, and record as formazin 

readings (pre-cal).

 e. Oil and wipe outside of daily Gelex®

standards, read, and record as Pre-cal 

Gelex® standard values.

 f. Insert a clean cell filled with reagent grade 

water. Press I/O.

 g. Press CAL. The CAL and S0 indicators 

will display and the 0 will flash. If the 

blank value was set to zero at the last 

calibration, then the display will be blank; 

otherwise, the value for the previous 

calibration will be displayed.

 h. Press READ. The meter will count from 

60 to 0 and then measure the turbidity. If 

using formazin standards, the meter will 

use the blank to calculate a correction for 

the subsequent standards. If the DI water 

used is >0.5 NTU, an E1 will appear. If this 

happens, clean cell and use new DI water. 

The display will automatically move to the 

next standard. Remove the 0 standard.

 i. The display will show S1 (with the 1 

flashing) and either 20 NTU or the value 

of the previous S1 standard. If using 

formazin and the value is incorrect, edit 

by pressing RIGHT ARROW until the 

number that needs editing flashes, then use 

the UP ARROW to scroll to the correct 

value. For StablCal® standards, it should 

read 20 NTU. Insert either a well-mixed 

formazin 20 NTU standard or the 20-NTU 

StablCal® standard. Press READ. The 

meter will count from 60 to 0, measure 

the turbidity, and then store the value. The 

display will automatically move to the next 

standard. Remove the cuvette.

 j. The display will show S2 (with the 2 

flashing) and either 100 NTU or the value 

of the previous S2 standard. If using 

formazin and the value is incorrect, edit 

by pressing RIGHT ARROW until the 

number that needs editing flashes, then use 

the UP ARROW to scroll to the correct 

value. For StablCal® standards, it should 

read 100 NTU. Insert either a well-mixed 

formazin 100-NTU standard or the 100-

NTU StablCal®standard. Press READ. The 

meter will count from 60 to 0, measure 

the turbidity, and then store the value. The 

display will automatically move to the next 

standard. Remove the cuvette.

 k. The display will show S3 (with the 3 

flashing) and either 800 NTU or the value 

of the previous S3 standard. If using 

formazin and the value is incorrect, edit 

by pressing RIGHT ARROW until the 

number that needs editing flashes, then use 

the UP ARROW to scroll to the correct 

value. For StablCal®standards, it should 

read 800 NTU. Insert either a well-mixed 

formazin 800-NTU standard or the 800-

NTU StablCal®standard. Press READ. The 

meter will count from 60 to 0, measure the 

turbidity, and then store the value. Remove 

the cuvette and press CAL to accept the 

calibration. The instrument will return to 

measurement mode automatically. 

 l. Immediately after performing the formazin 

or StablCal® standard calibration, remeasure any Gelex® standards used with 

this specific meter and record the new 

value on the Gelex® standard. Remember 

Gelex® standards are associated with a 

specific instrument; they cannot be used 

on another instrument without separate 

calibration for that instrument.

 m. Record the calibration on the calibration 

sheet and prepare a new control chart. 

 Check the Hach 2100P manual if any error 

messages occur or for more complete calibration 

instructions.

D.4 Velocity Meter (Marsh McBirney Model 201D)

 Maintenance and calibration requirements for 

the Marsh McBirney Model 201D include the 

following (see manufacturer’s instructions for a 

complete discussion):

 a. Move the selector switch to CAL position.

 b. Set the time constant switch to 2. After 

10 sec, the readout should be on or 

between 9.8 and 10.2. If it is not, check the 
D-7

battery pack connections and the batteries. 

If this does not resolve the problem, 

technical servicing may be required.

Notes:

 a. Never turn the selector switch past the 

CAL position when the probe is out of the 

water.

 b. Clean the sensor with clean water or mild 

dish soap and water if needed after each 

field day.

 c. Be extremely careful not to scratch the 

sensor surface in any way; treat it as if it 

were an optical surface.

 d. Do not store the meter for an extended time 

without removing the batteries.

 e. The sensor is delicate. Care should be 

taken when handling it, as banging or 

jarring of the sensor may cause serious 

damage.

D.5 Velocity Meter (Marsh-McBirney

Flo-matetm Model 2000)

 The Marsh-McBirney Flo-matetm Model 2000 

velocity meter requires limited maintenance 

and calibration. Calibration checks must be 

made at the factory, or by comparison to a 

recently calibrated meter at least annually, or 

whenever meter performance is questionable. 

Documentation of these performance checks 

and calibrations is maintained at the field 

station. It is essential to keep the sensor clean 

of any contaminants, especially oil and grease. 

Instructions in the instrument manual should be 

followed exactly for daily cleaning of the sensor 

and checking the zero point (Marsh-McBirney 

1994).
E-1

Appendix E. Equipment List for Water Quality Monitoring

 The equipment used in the Long Term Resource Monitoring Program (LTRMP) water quality 

monitoring has evolved over time (Table E-1). The items listed here are the typical configuration 

used by most field teams, but where other equipment has been documented to meet the necessary 

performance requirements it has occasionally been substituted by some participants. The following 

list does not constitute a commercial endorsement of the equipment or vendors by the LTRMP, the 

U.S. Geological Survey, or any LTRMP participants.

Table E-1. Major field equipment items used in the Long Term Resource Monitoring Program by water quality monitoring teams.

Manufacturer Model Description and use

Hydrolab Corporation, Loveland, Colorado

Minisonde4, Datasonde3 (phased out 

in 2002) 

Temperature, dissolved oxygen, specific 

conductance, pH

Omnidata International, Inc., 

Logan, Utah 

Polycorder 286LX handheld DOS 

computer

Data display for Datasonde3 

Phased out in 2002

Hach Company, Loveland, 

Colorado

2100P portable turbididmeter Nephelometer for turbidity measurements

Marsh-McBirney Inc.,

Frederick, Maryland

Flo-mateTM Model 2000 water 

flowmeter

Electromagnetic velocity meter

Marsh-McBirney Inc.,

Frederick, Maryland

201/201D portable water flowmeter Electromagnetic velocity meter

Biohit, Inc. Biohit Proline pipette fixed volume 

5,000 μL

Fluorometric chlorophyll-a volume

Itronix®, Spokane, 

Washington

XC6260 Pro Laptop PC, platform for electronic data 

sheet, and instrument interface

Itronix®, Spokane,

Washington

GoBook MAX TM Laptop PC, platform for electronic data 

sheet, and instrument interface
F-1

Appendix F. Previous Methods and Equipment

 This appendix describes selected procedures 

and equipment no longer used in the Long 

Term Resource Monitoring. This information is 

provided to help interpret historical data obtained 

with these methods and equipment and to guide 

operation of nonstandard equipment when 

necessary.

F.1 Previous Methods

F.1.1 Winkler Method for Dissolved Oxygen 

(discontinued in July 1997)

 The Winkler Method generates elemental 

iodine in proportion to the amount of dissolved 

oxygen in the original sample. This iodine 

is extremely volatile and is generated when 

the sample is acidified in step f below. After 

acidification, iodine can escape from the sample, 

and the dissolved oxygen as determined by the 

titration of the iodine will be erroneous (low). 

Excess iodide in the sample helps to stabilize 

the solution and reduces iodine losses, but the 

sample must be titrated without delay. The 

amount of iodine generated is measured by 

titration with thiosulfate solution. Thiosulfate 

solution, even when stabilized is not truly stable 

and its strength must be checked weekly against 

a standard biiodate solution (available from Hach 

Chemical, Loveland, CO; method described 

below).

 Water samples for the Winkler Method of 

dissolved oxygen determination are collected 

from a specific depth using a discrete sampler 

(Section 7.3) and then analyzed following 

Standard Methods (APHA 1992). The sample 

must not be agitated or allowed to come into 

contact with the air after collection. The sample 

is transferred from the sampling device to a 

biological oxygen demand (BOD) bottle (250 to 

300 mL) by a tube that extends from the sampler 

to the bottom of the BOD bottle. The BOD 

bottle is allowed to overflow with the sample 

for approximately 10 sec while minimizing 

turbulence and ensuring that no bubbles are 

formed. The BOD bottle is tilted slightly and a 

glass stopper wetted with leftover water from 

the sample is inserted so that no bubbles are 

entrained. 

 Chemical analysis of the bottled sample 

exactly follows the azide modification of the 

Winkler Method described in Standard Methods

(APHA 1992) and is described below. Collected 

samples should be fixed immediately by addition 

of manganese and azide reagents (injected below 

the sample surface). If the samples are quickly 

taken past the acid addition and properly watersealed, they can be stored in darkness and at 

temperatures between 20 and 30°C for up to 

12 hours before the remainder of the analysis is 

completed.

CAUTION: THE CHEMICALS USED 

FOR THE WINKLER 

METHOD ARE TOXIC AND 

CORROSIVE, SO BE SURE 

TO WEAR PROTECTIVE 

CLOTHING AND USE 

SAFE LABORATORY 

PROCEDURES.

a. Remove stopper and add 1 mL of the 

manganous sulfate first and then 1 mL of the 

alkaline iodide azide solution to each BOD 

bottle (add reagents in this order—inject 

reagents below the water surface in the 

bottle).

b. Insert the glass stoppers in the BOD bottles 

and mix by inverting gently. This should 

be done over a sink, as some overflow will 

occur when the stopper is inserted. Before 

proceeding to the next step, wait for the 

precipitate to settle until the upper third of 

the bottle contains only clear solution.

 c. After the precipitate has settled, remove the 

stopper from one BOD bottle, add one 3-g 

powder pillow of sulfamic acid (or 1 mL 

of concentrated sulfuric acid), and replace 

stopper on bottle immediately. Repeat for 

each BOD bottle. Gently mix by inverting 

the bottles until all solids are dissolved. This 

should be done over a sink as some overflow 
F-2

will occur. If necessary and if proper water 

seal is carefully maintained, the sample 

may now be held for up to 12 hours before 

proceeding with steps d–i.

d. Fill the titration buret with standardized 

sodium thiosulfate solution (0.025 N).

e. Pour the solution from the BOD bottle into 

a volumetric flask (203-mL polypropylene) 

and then into a 500-mL Erlenmeyer flask for 

titration. Begin to titrate IMMEDIATELY. 

The use of 203 mL instead of 200 mL is to 

compensate for the addition of fixing agents 

to the original sample volume. A volumetric 

flask is used instead of the entire BOD 

bottle volume because BOD bottles are not 

particularly precise in their dimensions.

f. Titrate the flask solution to a pale yellow 

color.

g. Add 2 drops of starch indicator to the flask 

solution. A blue color should appear.

h. Titrate carefully until the solution is clear.

i. REPEAT steps g–h for each BOD bottle.

 Each milliliter of sodium thiosulfate (at 

0.0250 N) used in the titration equals 1.0 mg/L of 

dissolved oxygen (DO). If the thiosulfate is not 

exactly 0.0250 N, then a correction factor must 

be applied (see below).

F.1.1.1 Thiosulfate Standardization

 A 200-mL sample (not 203 mL as used in 

DO titrations) of standard biiodate solution 

(0.00125 N; available from Hach Chemical in 

4-L bottles) is measured out with a volumetric 

flask and added to a 500-mL Erlenmeyer flask. 

A powder pillow (3 g) of sulfamic acid or 1 mL 

of concentrated sulfuric acid is added and the 

sample is swirled. The sample in the Erlenmeyer 

flask is now exactly equivalent to a 10-mg/L DO 

sample; proceed with the titration as in steps d–i 

above. Repeat this determination three times, 

recording the results. A correction factor for the 

actual strength of the thiosulfate solution is then 

calculated by dividing 10 by the average volume 

of titrant used in this standardization test (e.g., 

10.0/10.40 = 0.961). This correction factor is 

then applied to sample titrations performed with 

this thiosulfate solution. For example:

DO mg/L in sample = (milliliters of titrant) x 

(correction factor)

F.1.2 Nitrogen—Total Kjeldahl

 In the LTRMP, total Kjeldahl nitrogen (TKN; 

organic nitrogen plus ammonia nitrogen) is 

determined from an unfiltered sample. In the 

analysis, all forms of organic nitrogen are 

reduced (by Kjeldahl digestion) to ammonia, 

which is then measured quantitatively. Any 

ammonium or ammonia (NHx) present in the 

original sample becomes part of the TKN. A 

separate analysis for ammonia on an undigested 

portion of the sample is used to determine the 

concentration of NHx before digestion, and the 

concentration of organic nitrogen in the sample 

can be calculated by the difference. The LTRMP 

discontinued Kjeldahl nitrogen analyses after 

analytical responsibilities were transferred to 

the LTRMP laboratory from the Waterways 

Experiment Station in 1993. However, TKN can 

be estimated from subsequent measurements 

by subtracting NOx measurements from total 

nitrogen values.

F.1.2.1 Definition

 The TKN is defined as the total amount of 

ammonia or ammonium nitrogen (expressed as 

milligrams of elemental nitrogen per liter) that is 

detected after an unfiltered sample is subjected to 

Kjeldahl digestion (APHA 1992).

F.1.3 Nitrogen—Dissolved Kjeldahl

 Total dissolved Kjeldahl nitrogen (DKN; 

organic nitrogen plus ammonium nitrogen) is 

determined as for TKN (Section F.1.2), but a 

sample is filtered in the field for the analysis. 

This constituent was measured in the LTRMP 

from June 1991 to April 1993 (Appendix A).

F.1.3.1 Definition

 The DKN is defined as the total amount of 

ammonia or ammonium nitrogen (expressed as 

milligrams of elemental nitrogen per liter) that 

is detected after a filtered (0.45-μm membrane) 
F-3

sample is subjected to Kjeldahl digestion (APHA 

1992).

F.1.3.2 Sample Collection and Preservation

 An appropriate depth-discrete water sample 

(Section 7.3) is collected. The sample is filtered 

(0.45-μm membrane) and preserved with sulfuric 

acid (pH approximately 2.5; Section 7) and is 

held in the dark on ice (approximately 4°C), until 

shipped to the laboratory for analysis.

F.1.4 Nitrogen—Total Dissolved

 In the LTRMP, total dissolved nitrogen 

is not a separate analytical measurement, 

but is calculated by adding DKN and NOx

concentrations (see appropriate sections).

F.1.5 Phosphorus—Total Dissolved

 The “total dissolved” concentration of 

phosphorus includes all common chemical forms 

of the material, both particulate and dissolved, 

that pass through a 0.45-μm membrane filter. 

A single chemical digestion is used to dissolve 

and hydrolyze all common forms of phosphorus 

in a filtered sample to produce orthophosphate, 

which can then be measured precisely in a single 

chemical analysis.

F.1.5.1 Definition

 Total dissolved phosphorus (TDP) is defined 

as the total amount of reactive phosphorus 

(expressed as milligrams of elemental 

phosphorus per liter) that is detected with the 

ascorbic acid method (APHA 1992) after a 

filtered (0.45-μm membrane) sample is digested 

with persulfate under acid conditions (APHA 

1992).

F.1.5.2 Sample Collection and Preservation

 An appropriate depth-discrete water sample 

(Section 7) is collected. The sample is filtered 

(0.45-μm membrane), preserved with sulfuric 

acid (pH approximately 2.5), and is held in the 

dark on ice (approximately 4°C), until shipped to 

the laboratory for analysis.

F.2 Previous Equipment

 This section provides information on 

equipment that was used previously in the 

LTRMP for water quality monitoring so that the 

data that was collected with this equipment may 

be properly interpreted.

F.2.1 Cole-Palmer Model 4070 Conductivity Meter

 This section does not describe this instrument, 

but rather the methods used in the LTRMP for its 

calibration. Because the conductivity of standard 

potassium chloride (KCl) solutions varies with 

temperature, and some early model conductivity 

meters were not temperature compensated, a 

table (Table F-1) was provided to make this 

correction manually if necessary. This table 

was also used to verify the performance of the 

automatic temperature compensation feature on 

meters with this capability.

 When calibrating the instrument, a zero or 

low cal check is normally done first. This is 

accomplished by having the sensor dry in air or 

in distilled water. Select COND for display and 

Table F-1. Conductivity of a 0.005 M KCl (potassium chloride) 

solution at various temperatures. Conductivity at 25C is defined 

as 717.5 S/cm.

Temperature Conductivity

20 646

21 660

22 674

23 689

24 703

25 717.5

26 732

27 746

28 761
F-4

press the CAL LOW key. The unit will display 

00.0. Press the CAL LOW key again and the 

instrument will take a zero reading on each of the 

three ranges.

 The next step in calibration is to do a span or 

CAL HIGH. We first rinse the sensor thoroughly 

in distilled water and dry it so as not to cross 

contaminate the standard solution. Place the 

sensor in the calibration solution and allow the 

sensor to equilibrate for several minutes (stir 

sensor periodically). Select COND for display 

and press CAL HIGH key. The unit will display 

the value of the last calibration solution. If this is 

different than the solution value presently being 

used, adjust the display for the proper value with 

the UP or DOWN ARROW keys.

 There are several considerations when doing 

a span function. First, the value of the standard 

solution should be greater than 20% of the range 

selected (i.e., higher than 0.400 on the low range; 

higher than 4 on the midrange; between 40 and 

70 on the high range). The instrument must be 

operating on the same range as the calibration 

entry value. Assuming we will be using a 1.408-

mS/cm solution at 25°C, the instrument should 

be operating on the low (0–1.999 mS/cm) range 

before the CAL HIGH key is pressed for the first 

time. This must be verified because the unit will 

not change ranges once the calibration sequence 

is begun.

 Once the appropriate range is established 

and the CAL HIGH key is pressed, adjust the 

displayed value to that of the calibration solution. 

Pay attention to the position of the decimal point. 

It must correspond to the instrument’s selected 

operating range. When using the 1.408-mS/cm 

standard, the CAL HIGH value must be entered 

with three decimal places, otherwise the slope 

that is calculated will be in error. If the original 

CAL HIGH value is not on the appropriate range, 

just press the ARROW key that points in the 

correct direction of adjustment. The cal number 

will begin to change in that direction, slowly at 

first and then more rapidly. Watch the position 

of the decimal point. It will change as the 

decades change. When the decimal point is in the 

correct position for the desired range, release the 

ARROW key and then depress it again. This will 

slow the rate of change so that the desired value 

is not overrun by a large amount.

 It is good practice to disable the auto-shut off 

feature during a CAL HIGH procedure. This will 

keep the unit from turning off if the operator is 

diverted in the middle of the calibration. Once 

the calibration solution value has been inputted, 

press the CAL HIGH key again and the unit will 

establish a proper slope, store its new calibration 

data, and return to the measurement mode.

F.2.1.1 Daily Calibration

 The conductivity meter is calibrated daily 

using a 0.01 M KCl solution. The procedure is as 

follows:

 a. Set the MODE switch to SET K.

 b. Adjust the display to the correct cell 

constant by using a small screwdriver 

inserted through the hole in the back of the 

meter.

 c. Obtain a factory premixed KCl solution 

(certified to National Bureau of Standards).

 d. Rinse the cell with some of the solution.

 e. Place the cell in the solution.

 f. Set the MODE to mS.

 g. Measure the resistance or conductivity of 

the solution by adjusting the MODE to 

progressively more sensitive ranges until 

the highest possible reading is obtained.

 There is no need to correct the reading to 

25°C as the meter does this automatically.

 Maintenance of the conductivity meter 

involves daily cleaning of the cell in a mild dish 

soap.

 Winter maintenance includes keeping the 

cell and meter in an insulated box in a warm 

environment (Section 4.3).

 If the readings become erratic or when a 

sharp endpoint cannot be obtained, check the 

cell’s platinum electrode. If the black coating is 

flaking or dirty, the cell needs to be replatinized 

or replaced until it can be replatinized (remember 

to SET K for the new cell).

F.2.1.2 Replatinizing Procedure

 It is strongly recommended that this procedure 

not be attempted by field station personnel. The 
F-5

LTRMP will maintain limited ability to perform 

this procedure on equipment for which it is 

feasible.

 a. Clean the cell in a solution of l-g 

chloroplantinic acid and 12-mg lead acetate 

in 100-mL distilled water.

 b. Immerse the cell in the solution.

 c. Connect both probes to the negative side of 

a 1.5-V dry cell battery.

 d. Connect the positive side of the battery to 

a piece of platinum wire and dip into the 

solution.

 e. Continue the electrolysis until both probes 

are coated with platinum black.

 f. Rinse with distilled water.

 g. The cell is now ready for use.

F.2.2 Orion 230A pH Meter

 This pH meter recognizes standard buffers 

and has the temperature-pH information that 

appears on the buffer label already programmed 

into its internal memory. In autocalibrate mode, 

the meter will (a) recognize the type of buffer 

that it is in (if pH is even close), (b) determine 

the actual temperature of the buffer, and (c) use 

the corrected pH value of the buffer at that 

temperature to calibrate itself. For example, if 

you manually enter pH 10 for a standard buffer 

solution at 5°C (to get the meter within the 

appropriate range), you will see the pH jump 

to 10.26 when the meter completes its selfcalibration. Some have incorrectly interpreted 

this behavior as a malfunction of the instrument. 

In manual mode, the pH buffer values are 

FORCED into the instrument by pressing the 

YES key after each digit is entered. For correct 

results, these values must accurately reflect the 

pH of the buffer at that temperature. The primary 

purpose of manual mode is to allow the use of 

nonstandard buffers.

 Additional details are provided in the Orion 

instruction manual (part number 213376-001, 

1991 edition; pages 13–16).

 The LTRMP field stations reported frequent 

problems with the thermistor probe on this 

meter and with fouling of the pH electrode 

(unacceptably slow response or inability to 

calibrate). Frequent cleaning and checking of 

the probes were required. Replacement of the 

original probes with more robust versions was 

recommended.

F.2.3 Hach Model 16800 Turbidimeter and 

Hydrolab Datasonde 3® Equipped with Turbidity 

Sensor

 For Hach Model 16800 turbidimeters that 

are taken into the field, calibration must be 

checked against secondary (field) standards at 

each site or whenever the instrument is subjected 

to significant vibration or bouncing (i.e., during 

travel between sites). Calibrations are performed 

according to manufacturer’s instructions.

F.2.3.1 Daily Checklist

a. Check battery or power supply as applicable. 

When operating in cold weather, ensure that 

heater batteries are fully charged.

b. Perform a zero nephelometric turbidity unit 

(NTU) or stray light check as applicable.

c. Calibrate the instrument against an 

appropriate set of standards that adequately 

cover the range likely to be encountered 

in the field. If both low (approximately 

10 NTU) and high (100–1,000 NTU) 

turbidity conditions are likely to be 

encountered, the instrument should be 

checked in both ranges. With the Hach 

Model 16800, use the cell riser when 

measuring at the 100- or 1,000-NTU range 

and be sure that the dot on the cuvette faces 

forward. Note that the nominal value for 

secondary Gelex® standards is not precise 

and is instrument-dependent. The formazin 

equivalent for a specific combination of 

Gelex® standard and nephelometer must be 

determined at regular intervals (see below). 

Calibration values for Gelex® standards are 

marked on top of the cap. 

Note: All turbidity standards have a limited 

shelf life; only unexpired standards can be 

used for calibration. If calibration requires 

a major adjustment of the instrument, the 

secondary standard is checked against 

another set of secondary or primary 
F-6

(formazin) standards. If the instrument 

still does not function properly, the water 

quality coordinator should be notified to 

coordinate repair and replacement.

F.2.3.2 Method (Hach Model 16800)

 Grab samples for turbidity are collected 

using the appropriate depth-specific sampler 

(Section 7.3). The LTRMP does not require that 

turbidity measurements be made in the field, 

but turbidity should be measured at the time 

of collection or as soon as practicable to avoid 

changes in the sample characteristics that might 

result from particle precipitation, flocculation, 

dissolution, growth, or decomposition. If the 

measurement is delayed, samples are kept from 

freezing, held in the dark at about 4°C, and 

measured within 24 hours of collection. The 

steps for measuring turbidity on a grab sample 

are as follows:

 a. A grab sample is collected (Section 7) 

and inspected to ensure that it has not 

been contaminated with bottom sediment 

or contains large debris or vegetation 

fragments. If the bottom sediment has 

been disturbed or the sample is otherwise 

contaminated, then another sample is 

collected, either in an undisturbed section 

of the site or after the water current has 

cleared the disturbance.

 b. The sample should be gently inverted 

several times immediately before 

measurement. This resuspends any settled 

particulates without introducing air bubbles 

into the sample.

 c. The cuvette is rinsed with sample water, 

and then an appropriate volume of sample 

is carefully poured into the clean cuvette. 

Avoid creating air bubbles while pouring 

the sample, and do not handle the cuvette 

in the optical area as oils from the skin will 

cause an erroneous reading.

 d. Carefully wipe the cuvette with a piece 

of cheesecloth or other soft material 

(laboratory wipes may scratch the glass) 

and place into the nephelometer. Maintain 

a consistent orientation of the cuvette (i.e., 

one surface always facing forward).

 e. Record the turbidity measurement. If the 

reading is unstable (i.e., fluctuates more 

than ±5% because of settling of material 

or movement of large particles), refill the 

cuvette from the same, well-mixed, grab 

sample and repeat the reading. Allow 

the instrument to settle from the shock 

of cuvette movement before taking the 

reading (1–2 sec), but do not wait long 

enough for the material to settle from 

the sample (>5 sec). Be sure that the 

grab sample is properly agitated before 

refilling the cuvette (see step b). If highly 

unstable readings are encountered (not 

because of instrument malfunction), three 

determinations from the same sample 

container are averaged. However, if one 

of these readings deviates substantially 

(>20%) from the other two, disregard the 

deviant reading and take another.

 f. When turbidity is too high to measure 

directly (off scale), then a sample 

dilution is used. Dilution is performed 

with volumetric pipettes (1-10 mL), a 

volumetric flask (100 mL), and a beaker 

(150–250 mL). For a 0.1X dilution, 10 mL 

of the sample is added to a clean (not 

necessarily dry) 100-mL volumetric flask. 

Distilled water is then added to bring the 

total volume up to 100 mL. The flask is 

swirled when about one-half the distilled 

water is added and then again when threefourths of the distilled water has been 

added. The 100-mL mixture is poured into 

the beaker to ensure good mixing (do not 

introduce air bubbles). The diluted sample 

is then read in the turbidimeter as usual, 

with the reading divided by the dilution 

factor (e.g., 30 NTU/0.1 = 300 NTU in 

original sample). 

 If turbidity is still too high to read, a 

greater dilution factor must be used. DO NOT 

FURTHER DILUTE A SAMPLE THAT HAS 

ALREADY BEEN DILUTED—START FRESH. 

To achieve a 0.050X dilution, pipette exactly 

5.00 mL of a well-shaken sample into a clean 

(rinsed with distilled water) volumetric (100-mL) 

flask and add distilled water as above to make 
F-7

100 mL of mixture. The NTU reading in this 

example is divided by 0.05 (or multiplied by 20).

 If even greater dilution is needed (extremely 

unlikely), dilute 2.50 mL of original sample 

to 100 mL in the cleaned volumetric flask and 

divide the NTU reading by 0.025 (multiply by 

40).

 In the sample comment section of the data 

sheet, record the dilution volumes used (i.e., 

10/100). Keep in mind that dilution with distilled 

water can alter the particulate materials in the 

sample, so dilution should be kept to a minimum.

F.2.3.3 Comparison of Secondary Standards for 

Hach Model 16800

 The following section is applicable if 

secondary standards are used for field calibration. 

When field calibrations are required (i.e., with 

Hach Model 16800), each field station maintains 

two sets of secondary Gelex® standards. One 

set is normally used in the field, and the second 

set is kept in the laboratory. These two sets of 

standards are compared to each other monthly 

to verify their condition. Important notes: 

(1) turbidity standards have a limited shelf 

life; only unexpired standards can be used for 

calibration, and (2) Gelex® turbidity standards are 

not interchangeable among instruments (i.e., a 

single Gelex® standard may give slightly different 

turbidity readings in two properly functioning 

nephelometers that have just been calibrated to 

the same formazin standard).

a. Calibrate the nephelometer using the 

unexpired set of laboratory Gelex® standards 

for 100 and 10 NTU, remember to use the 

cell riser when measuring solutions in the 

100- or 1,000-NTU range and orient the dot 

on the cuvette so that it faces forward). The 

formazin equivalent values for the Gelex®

standards are recorded on the cap. If the 

nephelometer requires major readjustment 

to calibrate or if the instrument cannot be 

adjusted to the proper reading, then the 

nephelometer may be malfunctioning or 

the standards may be inaccurate. To resolve 

the source of the problem, attempt to 

calibrate the instrument using fresh formazin 

standards. If the instrument is the source of 

the problem, have it repaired or replaced. 

Replace defective laboratory standards 

after consultation with the water quality 

coordinator.

b. Insert the field secondary standard for the 

high range (80–100 NTU) and take five 

readings. Rotate the standard about 60° 

between readings. Repeat for the low NTU 

(5–10 NTU) field secondary standard.

c. Record the range of readings obtained with 

each field standard and the nominal value 

recorded on the cap.

d. If the average of the five readings differs 

from the cap value by greater than 5% or 

the range of values is greater than 10%, 

inspect the field standard for scratches, chips, 

fingerprints, bubbles, etc. If the standard is 

scratched, apply silicone oil to the scratch; if 

the vial is dirty, clean with distilled water and 

a piece of velvet or cheesecloth; if bubbles 

have formed, the standard is no longer usable 

and should be replaced. After cleaning or 

applying oil, remeasure the standard. If the 

difference between the cap value and the 

reading remains greater than 5%, the standard 

must be rechecked against a formazin primary 

standard (see below). If the range of five 

readings after cleaning and oiling exceeds 

10% of the average value, the secondary 

standard must be discarded. Substitute the 

laboratory standard for field use and order a 

new Gelex® standard for the laboratory. 

e. All preceding steps must be documented in 

the turbidity calibration and maintenance log 

book.

F.2.3.4 Calibration with Formazin (Hach Model 

16800 or Hydrolab Datasonde 3® Equipped with a 

Turbidity Sensor)

WARNING: FORMAZIN CAN BE 

HAZARDOUS TO YOUR 

HEALTH. ALWAYS HANDLE 

IT WITH RUBBER GLOVES

 This calibration is performed as required by 

the instrument being used. It is performed at 

least once per quarter or whenever the instrument 
F-8

or secondary standard does not calibrate 

satisfactorily. Formazin calibration is also 

required whenever the systems electronics or 

optics are significantly altered (i.e., lens cleaning, 

focus adjustment, potentiometer adjustment, 

etc.). 

 A formazin calibration is performed (and 

recorded in the turbidity calibration and 

maintenance log book) only after the instrument 

has received its daily check and routine 

maintenance (e.g., is properly focused, charged, 

and the lens cleaned) as follows:

 a. Following the guidelines in Table F-2, 

prepare formazin standards using 

volumetric flasks (500 and 1,000 mL), 

prepare 80- and 8-NTU dilutions

(4:200 and 2:1,000, respectively) from 

the concentrated formazin (4,000-NTU) 

standard. Use low turbidity water (i.e., 

filtered, deionized) and volumetric 

glassware (not graduated cylinders or 

transfer pipettes). Contrary to instructions 

in some instrument manuals, the LTRMP 

does not prepare turbidity standards by 

repeated dilutions. Each dilution must 

be prepared directly from the original 

(4,000-NTU) standard. The dilutions 

have a shelf life of only 2–3 hours, so the 

calibration process must be completed 

before that time has elapsed.

Table F-2. Instructions for preparation of formazin standards for 

specific nephelometric turbidity units (NTU).

NTU Dilution instructions

20 Pipette 1 mL of 4,000-NTU formazin into 

a clean 200-mL volumetric flask. Dilute to 

line with deionized water, insert stopper, and 

mix.

100 Pipette 5 mL of 4,000-NTU formazin in 

200-mL volumetric flask. Dilute to mark 

with deionized water and mix.

800 Pipette 20 mL of 4,000-NTU formazin in 

a 100-mL volumetric flask. Dilute to mark 

with deionized water and mix.

Note: Concentrated formazin standards have a 

guaranteed shelf life of only 1 year after 

receipt. They should be kept cool, held 

in the dark (i.e., in the refrigerator), and 

labeled with the date they were originally 

received, not the date they were opened. 

Be sure to use the unexpired standards 

for calibration. Use gloves and clothing 

protection when mixing formazin 

solutions. Wash hands immediately after 

any contact with formazin.

 b. Pour the entire volume of diluted standard 

from the volumetric flask into a clean 

beaker or flask that will allow the sample 

to be gently stirred. Swirl suspension 

gently to ensure uniform distribution of the 

formazin.

 c. Ensure that the nephelometer is properly 

zeroed and focused according to 

manufacturer’s instructions (as applicable).

 d. Insert standard (or submerge probe). 

Adjust the nephelometer according to 

manufacturer’s instructions.

 e. Remove the formazin standard and insert 

a comparable secondary standard into the 

nephelometer. Proceed as in steps b–d 

of the monthly comparison of secondary 

standards above.

 f. Repeat steps d and e for additional 

standards as appropriate.

 g. If appropriate (see manufacturer’s 

instructions), check the range or span 

calibration on the instrument while the 

formazin primary standards are still usable.

 h. Whenever internal adjustments, lamp 

replacement, or lens cleaning is performed, 

the instrument and its secondary (Gelex®) 

standards must be recalibrated against a 

formazin primary standard.
G-1

Appendix G. Sonde Holder for Use in Subfreezing Temperatures

 When sampling is performed under 

subfreezing conditions, multiparameter 

instruments, such as the Hydrolab Datasonde, 

must be kept from freezing, yet still be stored 

in an aqueous environment to prevent drying 

of the probes. Several options are available to 

achieve this depending on ambient temperatures. 

If conditions are only slightly below freezing, 

then an insulated tube with water initially at 

around 20–25°C should prevent significant icing 

problems throughout a day of sampling. For 

slightly cooler conditions, a small volume of 

alcohol may be added to the insulated tube to 

lower the freezing point (note that the pH will 

require longer equilibration time than normal 

when stored in alcohol).

 For extreme conditions (subzero Fahrenheit), 

a heated tube will prevent freezing of the sonde. 

The “Hot Tube” was developed specifically 

for use at the northern Long Term Resource 

Monitoring Program field stations and consists 

of an insulated “tube-within-a tube” design 

(Figure G-1). It runs off of a 12-V battery and 

provides a few watts of heat to prevent excessive 

icing in the tube. The thermostat is adjusted to 

keep the water in the tube at about 4°C, thereby 

eliminating long temperature equilibration times 

at each site. The Hot Tube can be constructed 

locally from PVC tubing, nickel-chromium 

wire (heating element), fiberglass insulation, an 

LED (to indicate “heating on”), and a simple 

thermostat.

Figure G-1. Heated tube used to hold multiparameter 

monitoring instrument in subfreezing temperatures.
H-1

Appendix H. Key to Subsurface Sampling Requirements for Off-Channel Areas

 This key can be used to determine if subsurface (>0.2 m) measurements or samples are required at 

a sampling location. The key is applicable to all areas (including MC) other than tributaries.

Is velocity 0.1 m/sec?

 Yes. No subsurface samples are required.

 No. Is there sufficient depth for a 

subsurface sample at least 0.2 m 

deeper than the surface sample (i.e., 

AWD 0.60 m)?

 No. No further samples required.

 Yes. In-situ measurements required. 

Does the difference between 

surface and bottom readings 

(0.2 m above sediment) meet any 

of the following criteria:

 (1)Temperature difference >1.9°C

 (2)Oxygen difference >3.9 mg/L

 (3)Specific conductance difference 

>50% of surface reading

 No. Record readings, but no 

subsurface water sample 

required.

 Yes. Is maximum depth (Zmax) 

>1.9 m?

 No. Record readings, 

but no subsurface 

samples required.

 Yes In fixed-site 

sampling only, 

water samples 

required for 

turbidity, suspended 

solids, and 

nutrients.
I-1

Appendix I. Program Code to Randomize Chlorophyll-a Sampling Sites

 This code is an example of a program that can be used with the SAS© software system to generate 

a randomized list of sampling sites. It uses a stratified random sampling location coordinates file as 

input. In this example, a location file for Pool 26, 2002, spring episode, primary sites is used.

Data Sites;

 * define the sites file;

 infile ‘c:\usr1\logfiles\SRSsites\P26w02so.dat’ dsd stopover;

 * read from the input file - site is a character variable; 

 input site $ stratum easting northing;

 * Assign a random number with a seed based on the clock;

 Rand1 = ranuni(-12345);

 run;

* Create a separate site order for each sampling stratum;

Proc sort data=sites; by stratum rand1;

run;

* Make a hard copy of the results;

Proc print;

title1 ‘Randomized Chlorophyll Calibration Sites’;

id stratum;

var site easting northing;

run;
J-1

Appendix J. Water Quality Forms

 This appendix provides copies of the forms 

(Forms J-1–J-8) used by water quality monitoring 

in the Long Term Resource Monitoring Program 

(LTRMP). Some of the forms shown here are 

provided only for reference and are no longer 

used routinely. All the forms are subject to 

change and the LTRMP water quality coordinator 

at the Upper Midwest Environmental Sciences 

Center (UMESC) should be contacted to obtain 

present version(s).

 From 1993 to 2003, the LTRMP database 

administration provided all the bar code labels 

used by the field stations. Every effort is made 

to ensure that bar code label sheets are properly 

printed and distributed to the field stations, 

but no system is completely foolproof and the 

accidental use of erroneous bar codes to label 

data or samples could have serious consequences. 

To provide a second level of error checking, each 

field station maintains a log of water quality bar 

code serial numbers received from the LTRMP 

staff at UMESC (Form J-6). As each new 

packet of bar code labels is received by the field 

station, the beginning and ending serial numbers 

in the packet are recorded in the field station 

log, and the entry is initialed by the individual 

making the log entry. In addition, each packet is 

inspected carefully to ensure that the two prefix 

digits in the serial number correctly indicate the 

component and field station. Any exceptions 

are brought immediately to the attention of the 

component coordinator who takes corrective 

action and issues a new packet of correct bar 

code labels. Erroneous bar code sheets are 

destroyed.

 The field data acquisition software 

(ScanLog32) may be used by field teams to 

print bar codes locally, but this feature had not 

been implemented as of the printing date of 

this manual. When implemented, it will permit 

local printing of bar codes, track bar code use, 

and guard against duplication of serial numbers 

(Form J-6). Field teams will still be required to 

exercise caution to ensure that the software is 

functioning correctly and that they are producing 

proper labels.

 In addition to daily calibrations, the 

performance of dissolved oxygen (DO) meters 

is routinely checked against another standard. 

During the first years of the Program, this was 

accomplished on a monthly basis by comparing 

DO meter readings to Winkler titrations 

performed on the same water. The Winkler 

procedures were problematic, so a replacement 

for the Winkler titration procedure was proposed 

(Memorandum dated January 20, 1997) and later 

implemented (May 1997). The new procedure 

provided a “bench sheet” (Form J-7) with stepby-step instructions for completing a quarterly 

performance test of DO and temperature probe 

functions. The new procedure compares the 

“air-calibration” technique, used for daily 

DO calibration, to readings taken in an airsaturated water bath. Strict limits for changes in 

atmospheric pressure, air temperature, and waterbath temperature must be met and documented 

before the cross-check is completed. The 

revised procedure provides further DO probe 

performance checks by testing anoxic response in 

a solution of sodium-sulfite/cobalt-chloride, and 

subsequent return to saturated-bath conditions 

(i.e., hysteretic error). Thermistor response is 

also compared during the quarterly procedure 

to a National Institute of Standards certified 

thermometer.
J-2

Form J-1. Multipurpose water quality data sheet.
J-3

Hydrolab Serial Number ________________

UP Calibration:

Date: _________ Hydrolab Date ___________ Reset (Y/N) _______

Time (CST): _________ Hydrolab Time ___________ Reset (Y/N) _______

DOWN Calibration:

Date: _________ Hydrolab Date ___________ Reset (Y/N) _______

Time (CST): _________ Hydrolab Time ___________ Reset (Y/N) _______

Conductivity: UP DOWN Dissolved Oxygen: UP DOWN

Hydrolab Reading (uS/cm): ______ ______ Temperature ______ ______

High Standard (uS/cm): ______ ______ Atmospheric Pressure (alt. corrected) ______ ______

Hydrolab reset to: ______ ______ Saturation Value from table (mg/L) ______ ______

Low Std (if required) ______ ______ Hydrolab Reading (mg/L) ______ ______

Hydrolab Reading ______ ______ Hydrolab Reset to (mg/L) ______ ______

pH: Turbidity:

Hydrolab Reading (7) ______ ______ Hydrolab Reading (NTU) ______ ______

pH 7 value @ temperature ______ ______ NTU Standard (NTU) ______ ______

Hydrolab Reset to ______ ______ Kaolin ______ ______

 Formazine ______ ______

 Other ______ ______ ______

Hydrolab Reading (10) ______ ______

 Hydrolab Reset to (NTU) ______ ______

pH 10 value @ temperature ______ ______

Hydrolab Reset to ______ ______

UP Calibration: External Battery Voltage ______ Internal Battery Voltage ______ Stirrer OK Y/N ______

Down Calibration: External Battery Voltage ______ Internal Battery Voltage ______ Stirrer OK Y/N ______

Remarks (e.g., servicing performed/questionable performance)

_________________________________________________________________________________________________________

_________________________________________________________________________________________________________

_________________________________________________________________________________________________________

Technician Performing UP Calibration: ___________________

Technician Performing DOWN Calibration: ___________________ EMTC 06/14/94

Form J-2. Long Term Resource Monitoring Program hydrolab calibration sheet.
J-4

Form J-3. Control charts with quality factor flags for documentating daily turbidimeter calibration drift
J-5

Form J-4. Missed site/missed parameter log sheet.

EMTC 06/14/94

Date Site Parameter missed Explanation
J-6

Field Station:_________________ Date: ______________

Name of Analyst:_________________ Serial Number: ______________

USFWS Number:_________________ Date last Charged: ______________

1. Review check list:

_____ 80 NTU formazine standard at room temperature

_____ 8 NTU formazine standard at room temperature

_____ Cuvettes clean and scratch free

_____ Meter warmed up at least 30 min

_____ Focusing template adjusted for proper light

_____ Zero point set and checked for all scales

_____ Span control set to midrange (10 turns counterclockwise, 5 clockwise)

2. 0–100 NTU RANGE

a. Insert cell riser

b. Insert 80 NTU formazine standard and adjust circuit board potentiometer to 

80 NTU reading

c. Remove formazine, insert Gelex®, and measure its value at three different 

orientations. Record each reading. Replace value on cap if necessary.

d. Prior Gelex® value: ________

e. Current readings: a.(dot forward) _______ b. ________ c. ________ 

3. 0–10 NTU RANGE

a. Remove cell riser

b. Insert 8 NTU formazine standard and adjust circuit board potentiometer to 8 NTU 

reading

c. Remove formazine, insert Gelex®, and measure its value at three different 

orientations. Record each reading. Replace value on cap if necessary.

d. Prior Gelex® value: ________

e. Current readings: a.(dot forward) _______ b. ________ c. ________ 

Comments:

 _______________________________

 Signature 

EMTC 06/14/94

Form J-5. Hach Model 16800 (nephelometer calibration with formazine).
J-7

Form J-6. Water quality bar code serial number log.

EMTC 06/14/94

Date packet 

received

Total number of 

label sheets

Replicates per 

serial number

Beginning

serial number

Ending

serial number

Initials of 

verifier
J-8

Form J-7. Quarterly dissolved oxygen meter calibration and performance check.
J-9

Form J-8. Monthly maintenance checklist for multiprobe instruments
J-10

Form J-9. Control charts with quality factor flags for documenting daily multiprobe calibration drift
The Long Term Resource Monitoring Program (LTRMP) for the Upper Mississippi

River System was authorized under the Water Resources Development Act of 1986 as 

an element of the Environmental Management Program. The mission of the LTRMP

is to provide river managers with information for maintaining the Upper Mississippi 

River System as a sustainable large river ecosystem given its multiple-use character.

The LTRMP is a cooperative effort by the U.S. Geological Survey, the U.S. Army Corps

of Engineers, and the States of Illinois, Iowa, Minnesota, Missouri, and Wisconsin.