U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2015–1188B

Toxic Substances Hydrology Program

Standard Operating Procedure for Collection of 

Soil and Sediment Samples for the Sedimentbound Contaminant Resiliency and Response 

(SCoRR) Strategy Pilot Study
Cover. Breach in the coastline at Rodanthe, North Carolina, caused by Hurricane Irene in August 2011. Photograph by Karen Morgan, 

U.S. Geological Survey.
Standard Operating Procedure for 

Collection of Soil and Sediment Samples 

for the Sediment-bound Contaminant 

Resiliency and Response (SCoRR) 

Strategy Pilot Study

By Shawn C. Fisher, Timothy J. Reilly, Daniel K. Jones, William M. Benzel, 

Dale W. Griffin, Keith A. Loftin, Luke R. Iwanowicz, and Jonathan A. Cohl

Open-File Report 2015–1188B

U.S. Department of the Interior

U.S. Geological Survey

Toxic Substances Hydrology Program
U.S. Department of the Interior

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2015

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Suggested citation:

Fisher, S.C., Reilly, T.J., Jones, D.K., Benzel, W.M., Griffin, D.W., Loftin, K.A., Iwanowicz, L.R., and Cohl, J.A., 2015, 

Standard operating procedure for collection of soil and sediment samples for the Sediment-bound Contaminant 

Resiliency and Response (SCoRR) strategy pilot study: U.S. Geological Survey Open-File Report 2015–1188b, 37 p.,

http://dx.doi.org/10.3133/ofr20151188B.

ISSN 2331-1258 (online)
iii

Contents

Abstract...........................................................................................................................................................1

Introduction.....................................................................................................................................................1

Background.....................................................................................................................................................2

Inorganic Geochemistry ......................................................................................................................2

Organic Geochemistry .........................................................................................................................3

Biological Assays..................................................................................................................................3

Pathogens ..............................................................................................................................................3

Purpose and Scope .......................................................................................................................................3

Sampling Methods.........................................................................................................................................3

Personnel Safety...................................................................................................................................3

General Field Safety ....................................................................................................................3

Sample Handling and Processing.............................................................................................4

Preparation ............................................................................................................................................4

Site Evaluation and Sampling Patterns.............................................................................................5

Sampling Equipment and Supplies ....................................................................................................5

Field Measurements.............................................................................................................................8

Sample Collection.................................................................................................................................8

Sampling Soil or Surficial Sediment .........................................................................................9

Sampling Bed Sediment ...........................................................................................................11

Filling Sample Containers..................................................................................................................13

Cleaning and Sanitizing Equipment .................................................................................................19

Quality Control During Sample Collection ......................................................................................20

Post Sample-Collection Procedure .................................................................................................21

Uploading Field Data .................................................................................................................21

Shipping Samples ......................................................................................................................21

Selected References...................................................................................................................................24

Glossary.........................................................................................................................................................27

Appendix 1. SCoRR Standard Operating Procedure quick reference guide..................................30

Appendix 2. Equipment and Supplies Checklist ..................................................................................34

Appendix 3. SCoRR Field Form—electronic version template .........................................................35

Appendix 4. SCoRR Field Form—manual entry template ..................................................................36

Appendix 5. SCoRR Cooler Inventory Form..........................................................................................37
iv

Figures

1. Aerial photograph showing an example of a grid created for collecting 

soil samples in wide areas that are uniform in soil and sediment 

consistency and potential for contamination, such as a field in a 

riverside park near Annapolis, Maryland .........................................................................................6

2. Aerial photograph showing an example of a spoke pattern for collecting 

marsh sediment samples in a large sample area with variable sediment 

conditions, such as the saltwater marsh at Wertheim National Wildlife 

Refuge, Brookhaven, New York..........................................................................................................6

3. Aerial photograph showing an example of a transect pattern created 

for collecting a beach sediment sample from a long, narrow sample 

area, such as a beach at Cape Cod, Massachusett .......................................................................7

4. Example of barcode label used on sample vessels for the Sedimentbound Resiliency and Response (SCoRR) pilot study.....................................................................7

5. Photograph showing the collection of soil temperature data.......................................................9

6. Photograph showing the collection of air temperature data ........................................................9

7. Photograph showing the collection of water parameters .............................................................9

8. Photographs showing examples of A, sample locations at sample types, 

and B, sample point preparations....................................................................................................10

9. Photographs showing steps for collecting and homogenizing soil in 

stainless steel and plastic bowls for organic and inorganic geochemistry 

analysis and archives.........................................................................................................................11

10. Photographs showing steps for collecting bed sediment samples using 

a Petite Ponar sampler ......................................................................................................................12

11. Photographs showing steps for collecting samples for pathogens 

analysis (sample container 01).........................................................................................................15

12. Photographs showing steps for collecting samples for inorganics 

screening analysis (sample container 02)......................................................................................16

13. Photographs showing steps for collecting samples for soil moisture 

analysis (sample container 03).........................................................................................................17

14. Photographs showing steps for collecting samples for methylmercury 

analysis (sample container 04).........................................................................................................17

15. Photographs showing steps for collecting samples for organics screening 

analysis (sample containers 05 and 06) ..........................................................................................18

16. Photographs showing steps for collecting samples for inorganics 

chemistry archive (sample container 07) .......................................................................................19

17. Photographs showing steps for collecting samples for organics chemistry 

archive (sample container 08) ..........................................................................................................20

18. Diagram showing chain of custody for samples collected for the 

Sediment-bound Contaminant Resiliency and Response (SCoRR) study .................................21

19. Photographs showing examples of foam shipping coolers packed to 

efficiently utilize space and minimize breakage for A, pathogen samples, 

and B, organic geochemistry samples (use the same method for inorganic 

geochemistry samples [not shown]) ...............................................................................................23

Tables

1. Minimum required physical parameters and observations at each 

sample location.....................................................................................................................................8

2. Sample requirements for soil and sediment collection................................................................14

3. Shipping destinations and preservation for samples collected under the 

Sediment-bound Contaminant Resiliency and Response (SCoRR) study .................................22
v

Multiply By To obtain

Length

centimeter (cm) 0.3937 inch (in.)

millimeter (mm) 0.03937 inch (in.)

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi)

kilometer (km) 0.5400 mile, nautical (nmi) 

meter (m) 1.094 yard (yd) 

Volume

liter (L) 33.82 ounce, fluid (fl. oz)

milliliter (mL) 0.03382 ounce, fluid (fl. oz)

liter (L) 0.2642 gallon (gal)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

 °F = (1.8 × °C) + 32

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 

(NAVD 88).

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).

Conversion Factors and Datums

EPA U.S. Environmental Protection Agency

GPS Global positioning system

HDPE High-density polyethylene

NOAA National Oceanic and Atmospheric Agency

NWIS National Water Information System

ODK Open Data Kit

SCoRR Sediment-bound Contaminant Resiliency and Response

SOP Standard operating procedure

USGS U.S. Geological Survey

Abbreviations

This Standard Operating Procedure (SOP) document is project specific, meant to be used 

in conjunction with the U.S. Geological Survey National Field Manual for the Collection of 

Water-quality Data, Book 9 (a USGS Techniques of Water-Resources Investigations [TWRI] 

publication). However, this SOP can be adopted for sampling efforts specific to storm-derived 

change for local and national programs outside of the SCoRR study.

Supplemental Information

Standard Operating Procedure for Collection of Soil and 

Sediment Samples for the Sediment-bound Contaminant 

Resiliency and Response (SCoRR) Strategy Pilot Study

By Shawn C. Fisher, Timothy J. Reilly, Daniel K. Jones, William M. Benzel, Dale W. Griffin, Keith A. Loftin, 

Luke R. Iwanowicz, and Jonathan A. Cohl

Abstract

An understanding of the effects on human and ecological 

health brought by major coastal storms or flooding events is 

typically limited because of a lack of regionally consistent 

baseline and trends data in locations proximal to potential contaminant sources and mitigation activities, sensitive ecosystems, and recreational facilities where exposures are probable. 

In an attempt to close this gap, the U.S. Geological Survey 

(USGS) has implemented the Sediment-bound Contaminant 

Resiliency and Response (SCoRR) strategy pilot study to 

collect regional sediment-quality data prior to and in response 

to future coastal storms. The standard operating procedure 

(SOP) detailed in this document serves as the sample-collection protocol for the SCoRR strategy by providing step-bystep instructions for site preparation, sample collection and 

processing, and shipping of soil and surficial sediment (for 

example, bed sediment, marsh sediment, or beach material). 

The objectives of the SCoRR strategy pilot study are (1) to 

create a baseline of soil-, sand-, marsh sediment-, and bedsediment-quality data from sites located in the coastal counties 

from Maine to Virginia based on their potential risk of being 

contaminated in the event of a major coastal storm or flooding 

(defined as Resiliency mode); and (2) respond to major coastal 

storms and flooding by reoccupying select baseline sites 

and sampling within days of the event (defined as Response 

mode). For both modes, samples are collected in a consistent 

manner to minimize bias and maximize quality control by 

ensuring that all sampling personnel across the region collect, 

document, and process soil and sediment samples following 

the procedures outlined in this SOP. Samples are analyzed 

using four USGS-developed screening methods—inorganic 

geochemistry, organic geochemistry, pathogens, and biological assays—which are also outlined in this SOP. Because the 

SCoRR strategy employs a multi-metric approach for sample 

analyses, this protocol expands upon and reconciles differences in the sample collection protocols outlined in the USGS 

“National Field Manual for the Collection of Water-Quality 

Data,” which should be used in conjunction with this SOP. A 

new data entry and sample tracking system also is presented 

to ensure all relevant data and metadata are gathered at the 

sample locations and in the laboratories.

Introduction

Enhanced dispersion and concentration of contaminants 

such as trace metals and organic pollutants through storminduced disturbances and sea-level rise are major factors that 

adversely impact the health and resilience of communities and 

ecosystems (Reilly and others, 2015). Infrastructure damage 

and chemical releases to adjacent waters can become associated with suspended sediments that are then deposited on 

shoreline soils, on beaches, and in the sediment of marshes 

and estuarine beds. Furthermore, pathogen outbreaks are often 

associated with sediment resuspension events, and extreme 

storm events can lead to food-web disruption and niche displacement (Plumlee and others, 2014). Overall, the presence 

of toxins and pathogens in contaminated soils and sediments 

can have environmental health implications in exposed populations of wildlife and humans.

The impacts to human and ecological health resulting 

from contaminants released during a major coastal storm or 

flooding event are difficult to measure without historical data 

and an established protocol for responding soon after the 

event. The U.S. Geological Survey (USGS) Sediment-bound 

Contaminant Resiliency and Response (SCoRR) strategy pilot 

study has been developed to demonstrate a sample-collection 

strategy to link the chemical, geological, and biological elements of a site. This means that a representative sample being 

collected from a site be handled according to the various sampling requirements of the respective analytical methods.

Sample collection conflicts that arise need to be reconciled from the perspective of data quality and should consider 

protocol complexity, staff time, reproducibility, preservation 

and shipping, cross contamination, and cost. The USGS 
2 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study

“National Field Manual for the Collection of Water-Quality 

Data” (U.S. Geological Survey, variously dated [b]) provides 

guidance on proper collection and handling of sediment 

samples, and procedures are focused on collection for organic 

or inorganic chemistry analyses with a standard shipping 

procedure. Considerations for the collection of data for genetics, bioassays, and inorganic and organic geochemistry from 

a single split sample require the various sampling procedures 

to be compatible so that the sample collection process is not 

onerous or introduces contamination. For example, the use of 

a Teflon-coated stainless steel spoon allows for a single tool 

to be used to sample for organic and inorganic geochemistry 

samples. Furthermore, samples are sieved by personnel at 

the receiving laboratories, which eliminates the need for two 

sieves in the field (stainless steel and plastic) and thus lessens 

the burden on the field crew (particularly when responding to 

a major storm or flooding event).

Standardizing the operating procedures for the USGS 

Water Science Centers (WSC) participating in SCoRR will 

provide consistent data quality and control throughout the 

study region. Techniques and methods from current Federal 

programs, such as the USGS National Water Quality 

Assessment and the U.S. Department of Agriculture (USDA) 

Soil Survey, are referenced throughout this standard 

operating procedure (SOP) document. This SOP provides a 

communication tool for the current field crew of SCoRR but 

can be modified for sampling efforts specific to storm-derived 

change assessment and used or adopted for local and national 

programs outside of the SCoRR study.

Background

As part of the response to Hurricane Sandy, USGS collected data on the effects of contaminant source disturbance 

and dispersion (Buxton and others, 2013). A major limitation 

of understanding the effects of Hurricane Sandy on contaminant transport and retention was the lack of regionally consistent baseline and trends data in locations proximal to potential 

contaminant sources and mitigation activities, sensitive ecosystems, and recreational facilities where human and ecological exposures are probable. As a result, the SCoRR strategy 

was implemented to compare current baseline conditions 

(defined as Resiliency mode) to conditions observed shortly 

after episodic stressors like a major coastal storm (defined as 

Response mode). A four-tiered approach has been developed 

to demonstrate the linkage between geospatial analyses used 

to identify potential sources of contamination (Tier 1) and subsequent qualitative (Tier 2) and quantitative (Tier 3) analytics 

used to document baseline (Resiliency mode) and event-based 

(Response mode) environmental conditions (Reilly and others, 

2015). Repeated Resiliency mode sampling and analysis allow 

for evaluation of incremental changes anticipated to occur as 

a result of sea-level rise and land-use changes. Subsequent 

biological uptake, fate, transport, and exposure studies 

(Tier 4) can be designed and prioritized based upon SCoRR 

strategy findings.

Sampling locations are identified using a decision support tool (from a geographic information system [GIS]) that 

considers the potential contaminant threat and vulnerability 

proximal to a potential station and stakeholder input (see 

Reilly and others, 2015, for description of site identification 

under Tier 1). Following site prioritization, a composite of 

surficial samples is collected at each site based on the matrix 

(soil, surfacial sediment, or bed sediment) of interest in the 

area. The current study area is the coastal counties (as defined 

by National Oceanographic and Atmospheric Administration 

[NOAA]) from Maine to Virginia, with USGS Water Science 

Centers from each State within the area participating in the 

sample acquisition during Resiliency mode and specialized 

teams during Response mode.

All samples collected under SCoRR are screened at 

USGS laboratories to qualitatively assess the inorganic 

geochemistry (including mineralogy, major ions, and metals), 

organic geochemistry (for attributes such as molecular structure and spectrophotometric response), ecological effects 

(including biological assays), and pathological composition 

(presence/absence and quantification of over 40 bacteria and 

virus populations). Results from this screening (Tier 2) inform 

the process of selecting a subset of samples to be assessed 

more rigorously (for example, chemical compounds identified 

and quantified) as part of Tier 3. In Resiliency mode, a fraction 

of total samples will be subjected to Tier 3 analysis, whereas 

all samples collected in Response mode will be subjected to 

analysis under Tiers 2 and 3. Many of the screening methods 

being selected for this study were evaluated during the 

regional sediment-quality reconnaissance conducted as part 

of the USGS response to Hurricane Sandy; references to these 

methods can be found in Fischer and others (2015). The following summarizes the analyses conducted as a part of Tiers 2 

and 3.

Inorganic Geochemistry

Screening methods will evaluate metals and trace elements at concentrations in the hundredths of parts per million 

(ppm) for qualifying leachable metals and major ions associated with soil and sediment, as well as those that comprise the 

media, and are used to classify the soil and identify any potential sources of contamination from anthropogenic sources. 

Instruments used for these analyses include x-ray fluorescence 

(XRF) to determine the relative percentage concentration of 

metals and x-ray diffraction (XRD) to determine the relative 

percentage mineralogy. Total carbon, total organic carbon, 

and total inorganic carbon concentrations are measured, as 

is the particle-size distribution of the materials. Changes to 

the properties of deionized water, simulated lung fluid, and 

simulated seawater solutions upon introduction of the sample 

are tested—in particular, change in pH and concentration of 

metals and major ions in solution.
Sampling Methods 3

Organic Geochemistry

Organic compounds associated with anthropogenic contaminant sources (such as those common to industrial, commercial, and residential land uses) are identified and discerned 

from naturally occurring organics. Methods used for screening sediment for organic compounds include attenuated total 

reflectance-Fourier transform infrared spectroscopy 

(ATR-FTIR), liquid chromatography ultraviolet/fluorescence 

spectroscopy. Quantification of organic compounds (and 

respective degradates) identified in Tier 2 analyses is conducted using liquid chromatography ultraviolet/fluorescence 

spectroscopy, time-of-flight mass spectroscopy (LC/UV-Vis 

fluorescence/TOF-MS) under Tier 3.

Biological Assays

Enzyme- and whole cell-based assays are employed to 

determine potential adverse environmental health outcomes 

associated with sediment-bound contaminants. Endpoints 

include toxicity, Microtox genotoxicity and mutagenicity, 

nuclear receptor transactivation/translocation, metallothionein 

gene transcription, and enzyme inhibition. Bioassay screening 

is performed on sediment extracts per Ciparis and others 

(2012), Knapen and others (2007), and Stavreva and others 

(2012).

Pathogens

While naturally occurring pathogens are common in 

sediments, elevated levels of human-borne pathogens can be 

indicative of contributions from failed wastewater treatment 

facilities, aging septic systems, or combined sewer systems. 

A presence/absence real-time polymerase chain reaction assay 

(PCR) is used to screen samples for select pathogenic viruses 

and antibiotic-resistance genes (ARG). Digital PCR analysis 

is used to quantify detected pathogens and ARG. For Tier 3 

analyses, select samples (those containing multiple pathogens 

or ARG) are further screened using genetic chip-based analyses, which will allow the identification of a comprehensive 

list of select bacterial, fungal and viral pathogens, and general 

ecological community composition. Following review of the 

data, results are interpreted as they relate to this demonstration of the SCoRR strategy and will also augment an ongoing 

nationwide assessment of pathogens and how they relate to the 

various soil and associated chemical composition (Griffin and 

others, 2014).

Purpose and Scope

In order to ensure a consistent sampling protocol 

throughout the SCoRR study area, this SOP has been created 

to describe, in detail, the manner in which samples are to be 

obtained, including all aspects of field preparation, safety, 

sample collection, and proper sample storage and shipping. 

This SOP serves to outline and describe the procedures and 

protocols for sampling soil, sand, marsh sediment, and bed 

sediment for the field crews supporting SCoRR in order to 

provide consistent data quality and control throughout the 

study region. This SOP can also provide a guide for other 

USGS projects and programs.

Sampling Methods

Field manuals for a variety of sampling procedures exist 

within the USGS and elsewhere; however, this SOP was 

created to provide instructions on sampling soil, sand, marsh 

sediment, and bed sediment for four suites of analyses, each 

with differing methods. In order to reconcile differences of 

sampling methods for inorganic geochemistry (including 

analysis for methylmercury), organic geochemistry, pathogens, 

and bioassay techniques, samples are split into a stainless steel 

bowl and a plastic bowl using a single, Teflon-coated stainless 

steel spoon. Samples are collected as composites across 

various coastal landscapes, thus techniques for choosing the 

proper sample pattern are described. Also employed for this 

pilot study is an app-based electronic field form and the use of 

barcoding, both of which were designed to minimize data loss, 

transcription error, and time in the field.

Techniques and methods adopted from current Federal 

program manuals, such as the guidelines for the USGS 

National Water Quality Assessment program (Shelton and 

Capel, 1994), the USGS “National Field Manual for the 

Collection of Water-Quality Data” (U.S. Geological Survey, 

variously dated), the U.S. Environmental Protection Agency 

(EPA) and USGS “Sample Collection Protocol for Bacteria 

Pathogens in Surface Soil” (Bowling and others, 2014), 

and the “Soil Survey Program” by the U.S. Department of 

Agriculture (2015), are referenced throughout the report. 

Selected procedures described in following sections are summarized in Appendix 1 to provide reference during sampling. 

Personnel Safety

General Field Safety

Field crews are to collect samples from a site only if the 

area is secure and it is safe to do so (that is, personnel are not 

put in harm’s way because of a situation beyond those encountered during normal operations)—particularly when sampling 

during Response Mode (post storm). Like all environmental 

samples, the material collected may contain chemicals and (or) 

pathogens of known and unknown toxicity to humans that are 

present as a result of adjacent land use and (or) storm damage 

and should be treated accordingly. Field personnel should 

be familiar with the USGS “Occupational Safety and Health 
4 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study

Program Requirements Handbook” (U.S. Geological Survey, 

variously dated [a]), the safety protocols and procedures outlined in chapter A9 of the USGS “National Field Manual for 

the Collection of Water-Quality Data” (Lane and Fay, 1997), 

as well as any activity- or site-specific training offered by 

USGS. Only staff with the appropriate sample collection and 

field safety training should be engaged in field work associated 

with SCoRR.

Per USGS requirements, a Job Hazard Analysis document 

outlining the potential risks associated with sampling must 

be completed and kept on file at each field office for personnel collecting data for SCoRR and should be available during 

sample collection. Standard safety protocols are to be followed 

when sampling from a boat (for example, dedicated captain 

and at least one person to sample with all wearing approved 

personal floatation devices), and a USGS Float Plan should 

be filed with the USGS WSC Safety Officer prior to departure 

each day or as required by the WSC. Sampling in, over, or 

in close proximity to water requires appropriate training and 

the use of an approved personal flotation device at all times. 

Guidelines in the U.S. Department of Labor Occupational 

Safety and Health Administration (OSHA) training should also 

be followed when working in disaster areas, such as following landfall of a major storm where significant damage has 

occurred (https://www.osha.gov/dte/outreach/disaster/index.

html).

Sample Handling and Processing

Sample sites may be contaminated with harmful chemicals or pathogens, particularly as a result of infrastructure 

damage following a major storm. It is important that the field 

crew is conscious of this potential and uses the appropriate 

safety and personal protective equipment for a given threat. 

An OSHA-approved face mask and safety glasses or goggles 

should be worn when dust or fine particles are suspended in 

the air. At a minimum, all personnel collecting or handling 

samples should be wearing two pairs of nitrile gloves—one 

as a base layer and one that gets changed. Ideally, two personnel are onsite to collect each sample and follow the USGS 

Clean Hands/Dirty Hands procedure outlined in chapter A4 

of the USGS “National Field Manual for the Collection of 

Water-Quality Data” (U.S. Geological Survey, 2006). For 

this procedure, one sampler acting as Clean Hands handles 

only the sample supplies that come in direct contact with the 

sample, and the other sampler acting as Dirty Hands handles 

the supplies that could come in contact with potential sources 

of contamination (U.S. Geological Survey, 2006). The USGS 

personnel collecting samples should be properly trained on 

sample collection through one of the approved courses offered 

by the USGS National Water Quality Laboratory.

As the biological activity and chemical composition of 

sediment samples will be assessed, care should be taken as 

to not introduce contaminants to the samples being collected. 

This includes but is not limited to volatile organic compounds 

from fuels and solvents; nicotine and other products from 

cigarettes and chewing tobacco; caffeine from beverages; 

surfactants and fragrances from personal care products; and 

microbes from coughing, sneezing, breathing, or stepping on 

the samples or in the sample area, as described in chapter A4 

of the USGS “National Field Manual for the Collection of 

Water-Quality Data” (U.S. Geological Survey, 2006). Refer 

to the “Quality Control During Sample Collection” section 

for additional details on the collecting of an uncompromised 

sample.

Preparation

Depending on the study area, the collection of a soil 

sample may require a research or sample-collection permit 

from local, State, or Federal agencies or permission from land 

owners. Soil collection and transport also may require permits 

issued by the USDA, which outlines guidelines for the proper 

handling and shipment of soils from areas with the potential 

for spreading invasive species (check with local USDA officer 

or visit the USDA Web site [referenced in the “Selected 

References” section] for a list of quarantined States). The 

USDA soil permits are typically issued in conjunction with the 

respective State health or environmental agency and are on file 

at all USGS laboratories currently involved with the SCoRR 

study.

In addition to this SOP, personnel should be familiar with 

the bottom-material (that is, bed sediment) collection protocol 

outlined in Radtke (2005) and Shelton and Capel (1994) for 

sampling for chemical analyses, and Bowling and others 

(2014) for sampling for biological analyses. This SOP also 

references “The Environmental and Medical Geochemistry 

of Potentially Hazardous Materials Produced by Disasters” 

(Plumlee and others, 2014) and the “Sample Collection of Ash 

and Burned Soils from the October 2007 Southern California 

Wildfires” (Hoefen and others, 2009), as well as the USGS 

Hurricane Sandy, Theme 4, marsh- and bed-sediment sampling 

standard operating procedures (Irene Fisher, USGS, written 

commun., 2013), which was followed for collecting samples 

during the USGS Hurricane Sandy ecological and human 

health assessment in 2013 (Fischer and others, 2015).

During Resiliency mode, sample collection can be spread 

out over several months in order to accommodate field crew 

schedules, stakeholder needs, and other considerations. The 

entire network should be sampled within a single season for 

consistency among sites and should be sampled in the same 

season for the entire study region (for example, the northeast 

region). The collection of samples also should be scheduled 

from Monday to Thursday to ensure overnight delivery (laboratories used for the SCoRR project do not accept samples on 

Saturday). However, during Response mode, stations should 

be identified as soon as possible and routes to each site should 

be planned as crews mobilize. Samples of soil and sediment 

should be collected as soon as possible (when safe) following a major storm and (or) flooding event in order to preserve 

and capture the potential changes that have occurred at the 
Sampling Methods 5

site (Plumlee and others, 2014). The collection of samples 

under Response mode should be scheduled from Monday to 

Wednesday to ensure overnight delivery if shipping to and 

(or) from disaster-affected areas. A list of alternative stations 

should be in place for the Resiliency and Response modes 

in the event that a site is not accessible because of traffic, 

roadway damage, or police closure. If a site is temporarily 

not accessible, crews should be prepared to visit the site later 

or on a different day. If a site is permanently blocked, or 

the required amount of sample cannot be collected from the 

immediate area, crews should be prepared to proceed to an 

alternate station.

Overnight shipping facilities close to the sample sites 

should be located before departing for the field. Ice supply 

should also be considered for field trips requiring one or more 

overnights. The frozen gel packs supplied for shipping pathogen samples should be kept in ice when traveling and would 

be better stored in a room freezer (if available) overnight.

Site Evaluation and Sampling Patterns

The location and sample media dictate the method for 

sample collection used at each site. Samples of soil and surficial sediment (for example, marsh sediment and beach sand) 

are typically collected without special equipment, whereas 

collection of bed sediment in areas with water overlying the 

sediment requires samples be collected by wading in on foot 

or from a bridge, dock, or boat. At each site, multiple grab 

samples are collected to create a composited sample. The distribution of the individual composite samples will depend on 

the extent and accessibility of each location. A decision should 

be made prior to arrival at the site as to which sample pattern 

should be employed (grid, spoke, or transect) using satellite 

images offered by online mappers, a reconnaissance trip, or 

institutional knowledge of the site; however, a different pattern 

and (or) method may need to be used by the field crew upon 

arrival if the site has been recently disturbed (for example, 

construction) or covered by water (for example, a tidal marsh).

Figures 1–3 provide examples of the three sample site 

patterns that can be employed for collecting a composite 

sample. The distances depicted in figures 1–3 are examples 

and can be as short as 10 feet (ft) apart for this study, depending on desired extent of sample area, and the fewest number 

subareas from which composites are collected is five. 

Ultimately, professional judgement is required for determining 

the number of subareas to be sampled at a site to ensure a representative sample for the sample area (Radtke, 2005; Shelton 

and Capel, 1994). Per the USGS National Field Manual for the 

Collection of Water-Quality Data, chapter A8 (Radtke, 2005), 

subareas are selected at each SCoRR study site by using either 

a systematic regular interval for establishing a grid, a transect 

pattern based on site characteristics, accessibility, and the total 

desired area to be sampled (for example, an entire shoreline 

field or a particular stretch of public beach bordering homes), 

or a nonstatistical deterministic method for spokes pattern or 

bed sediment sampling (Radtke, 2005).

Sample collection using a grid pattern is employed in 

uniform fields or a coastal community (developed area) where 

soil (or other media) can be collected near the center of each 

box (fig. 1). The boxes that comprise the grid can vary in size 

and shape depending on the total amount of sampling area 

and desired extent of sample area away from the prioritized 

station. Figure 2 illustrates the spoke diagram, which is well 

suited for sampling in marshes because each sample away 

from the centroid can extend out to capture or avoid particular 

features, such as mosquito ditches or pannes. The lengths of 

each spoke (that is, the distance from the centroid) shown in 

figure 2 should remain the same at a given site, but can vary 

from site to site. The number of composite points (or subareas) should also be evenly divided to get equal angles from 

the centroid. The transect pattern shown in figure 3 is useful 

when the desired sample area is a long, narrow strip of land 

(for example, a beach) or from the coast inland. A transect 

should start at the station coordinates identified and proceed in 

a single direction, with samples for the composite collected at 

set increments.

Sampling Equipment and Supplies

Equipment and supplies needed for sample collection 

are listed in Appendix 2. It is important to ensure all 

sampling equipment is functioning properly, free from rust 

and corrosion, and thoroughly cleaned (and sanitized if 

needed for pathogen sampling) prior to leaving for the field. 

Thermometer(s) used in the field (for air and soil) should be 

checked for accuracy at the beginning of the sampling season 

and calibrated every 12 months using a National Institute of 

Science and Technology traceable as described in the USGS 

Field Manual (Wilde, variously dated). Multiparameter 

water-quality sensors should be checked and calibrated using 

approved standards prior to use in the field with calibration 

records properly documented (for example, in a USGS 

logbook).

The Garmin (Olathe, Kansas) MonterraTM was selected 

for use in this study because it is an all-in-one handheld device 

that provides the ability to acquire position through Global 

Positioning System (GPS) satellites (as opposed to cellularbased triangulation), take pictures of sampling locations, 

scan barcodes on sample containers, and the functionality to 

allow for field data to be entered electronically. (A handheld 

GPS, camera, and laptop/paper field forms can be used if a 

MonterraTM is not available.) The GPS data are collected using 

the North American Datum of 1983 (NAD 83), and an accuracy of plus or minus 10 ft should be achieved before accepting the location coordinates. The GPS device should be turned 

on and actively searching for satellites for as long as possible 

before accepting the location (a GPS accuracy of 10 ft or less 

is acceptable). Therefore, it is best to turn the device on upon 

arrival at a site (or earlier).

The SCoRR field form (framework of the electronic version shown in Appendix 3, and a printable [back-up] version 
6 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study

EXPLANATION

Sample site for

composite

Station

EXPLANATION

Sample site for

composite

Station

Figure 1. Example of a grid created for collecting soil samples in wide areas that are uniform in soil and sediment 

consistency and potential for contamination, such as a field in a riverside park near Annapolis, Maryland.

Figure 2. Example of a spoke pattern for collecting marsh sediment samples in a large sample area with variable 

sediment conditions, such as the saltwater marsh at Wertheim National Wildlife Refuge, Brookhaven, New York.
Sampling Methods 7

is shown in Appendix 4) must be completed and submitted 

electronically in order to process a sample and generate a 

reference number. The electronic field form application was 

created using a free, open-source program developed by Open 

Data Kit (ODK) (https://opendatakit.org/), which uploads 

all acquired data to the formhub.org server. A database of 

the identified sampling stations is provided by the SCoRR 

network coordinator prior to start of the sampling effort (in 

Resiliency mode and when Response mode is activated). Each 

field crew should download the prioritized stations set for their 

region for the field form to query; instructions are provided to 

the lead sampler in advance of the sampling effort. The field 

form requires a basic description of the location, latitude and 

longitude, a representative picture of the sampling location, 

and a date/time. Depending on the device (if not using the 

MonterraTM), most of these fields are populated automatically 

by clicking on the “auto fill” box; otherwise, additional equipment (GPS and camera) will be required and uploaded separately following sample collection, but prior to upload.

The default barcode reader application will be activated 

by the electronic field form (the number is also printed on the 

label should manual entry be necessary). Sampling containers 

are to be pre-labelled with a barcode (this study uses the 

standard Code 39 symbology) that has a sample-set-specific 

serial number, with the last two numbers representing the 

container code of the eight sample containers in sequential 

order (01–08). Figure 4 is an example of the sample container 

label indicating the state (“NY”) from which the sample was 

collected, the six-digit unique sample-set identifier (123456) 

that will be automatically attributed to the data entered into the 

field form, and the two-digit analysis code that is designated 

by the container type (02). Note that the hyphens used to break 

up the alphanumeric serial number displayed on the label are 

not coded into the barcode (that is, label text NY–123456–02 

is stored as “NY12345602” in the database). As codes are 

sample, not station, specific, any sample set can be used 

(within the state identified) at a site.

The barcode serves to automate the data transfer process 

and will document the chain of custody through the sampling 

and analyses steps associated with this project. Once samples 

are received by the analyzing laboratories, the containers will 

be scanned to automatically generate an entry in the laboratory 

Figure 3. Example of a transect pattern created for collecting a beach sediment sample from a long, narrow 

sample area, such as a beach at Cape Cod, Massachusetts.

Figure 4. Example of barcode label used on sample vessels 

for the Sediment-bound Resiliency and Response (SCoRR) 

pilot study.

EXPLANATION

Sample site for

composite

Station

Inorganics

SCoRR

N Y – – 1 2 3 4 5 6 0 2

2015

250mL HDPE 3⁄4-full
8 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study

results database, into which data from each analysis will be 

linked to the field forms when queried. The inorganic and 

organic geochemistry laboratories will conduct chemical 

extractions of the sediment per their respective methods and 

send extracts to the bioassays laboratory for analysis—no 

samples are shipped from the field directly to the bioassays 

laboratory. For field blanks submitted to the pathogen laboratory, a sample set with an additional vial coded 01B should 

be used; alternatively, a spare label can be used as long as 

the sample set along with 01B is written on the label (see the 

section “Quality Control During Sample Collection” for more 

information about field blanks). Vials containing extracts 

from the original sample jars will be labeled by the organics 

and inorganics laboratories with a barcode encoded with the 

sample identity and an “E1” for “extract [number] 1”; subsequent extracts from the same container (if necessary) will have 

sequential numbers following the “E.”

A standard cooler should be filled with enough ice to 

ensure samples remain chilled in the field, frozen ice packs 

remain frozen, and shipping coolers can be filled properly (if 

shipping from the field). In addition to the set of frozen gel 

packs placed in the small foam shipping cooler to keep the 

vials for pathogen analysis chilled in the field, sets of frozen 

gel packs equal to the number of small shipping coolers 

expected to be shipped should be packed is a large zip-top bag 

and kept in ice if shipping from the field. Arrangements should 

be made prior to departing for long field days or multiple-day 

field trips to ensure availability of ice necessary for the aforementioned uses.

Field Measurements

Prior to collecting samples, the field crew should position 

themselves at the first sampling point (station) in the pattern 

to complete the electronic field form, which includes recording GPS data, collecting field parameters, and taking at least 

two field photographs. Physical parameters of soil, air, and 

water (if applicable) are to be collected at all sample sites 

using a thermometer and multiparameter water-quality sonde 

(Appendix 2). The minimum required parameters are listed 

in table 1 and on the field form. (Additional measurements 

may be collected and documented along with their respective 

USGS parameter codes in the “Notes” section of the field 

form.)

Sample Collection

Sample collection protocol involves collecting eight 

samples, each with their own collection requirements. One 

container is directly filled with sediment, and other containers 

require the composite sample from multiple subareas in a 

pattern from a site to be homogenized and then distributed 

into containers. The steps listed below outline these collection 

requirements and are critical for the site preservation and quality assurances for the laboratories.

Collecting soil or surficial sediment and filling sample 

containers can be done by an individual sampler, but a crew 

of two qualified sampling personnel is optimal. When two 

sampling personnel are onsite, one crew member is responsible for preparing the site, organizing the sampling materials, 

and keeping the sample containers and labels clean and free 

of contaminants. The other crew member should focus on 

collecting the sample, keeping track of the amount of sample 

collected, and ensuring that the sample site does not become 

contaminated (U.S. Geological Survey, 2006).

Barcodes for the jars should be scanned prior to being 

filled, and care should be taken to not get the sample on the 

label while filling because it could interfere with barcode reading in the laboratory. If a jar cannot be scanned, the code can 

be entered manually using the keypad; type in the sample jar 

serial number below the barcode (without hyphens). If a container is lost or broken during sample collection, fill a replacement jar and write the sample set code and container number 

on a new waterproof label and attach to the jar (if original jar 

Table 1. Minimum required physical parameters and observations at each sample location.

[Physical parameters associated with the sample area are to be documented prior to collecting samples. Observations of weather, sky, and wind at sample 

location are qualitative with basic responses outlined on the field form. USGS, U.S. Geological Survey; °C, degrees Celsius; --, not applicable; ft, feet; 

μS/cm, microsiemens per centimeter at 25 degrees Celsius; mg/L, milligrams per liter]

Media Parameter Units USGS parameter code Reference figure

Soil or sediment Soil temperature °C -- Figure 5

Air

Air temperature

Weather

Sky

Winds

°C

--

--

--

00020

--

--

--

Figure 6

Water 

(at sample depth)

Depth to bottom

Water temperature

Specific conductance

pH

Dissolved oxygen

ft

°C

μS/cm

pH units

mg/L

81903

00010

00095

00400

00300

Figure 7
Sampling Methods 9

was lost), or carefully remove the label from the old jar and 

adhere it to the replacement (only attempt to remove label 

from a broken jar if there is no risk of being cut by broken 

glass; otherwise, create a new label). A spare set of sample 

containers should always be included with field equipment in 

case of breakage or loss.

Sampling Soil or Surficial Sediment

1. Identify the area from which soil or surficial sediment 

is to be sampled and follow the pre-determined sample 

pattern (examples of sample patterns are shown in 

figs. 1–3) chosen for the site. If site is on the shoreline, 

locate the high tide mark (or rack line); samples are 

to be collected upland from this mark (fig. 8A). Also, 

make a plan that includes the path for approaching 

and exiting each subarea for collecting the composite 

samples. Once a site is cleared and prepared, your foot 

pattern must avoid collection points.

2. Put on disposable shoe covers; take care not to step on 

or otherwise compromise the point within each subarea 

identified for sample collection. (Note that shoe covers 

are not needed on a boat or may not be practical in a 

marsh, in which case, take extra precautions not to step 

on or too close to the sampling points.)

Figure 5. The collection of soil temperature data.

Figure 7. The collection of water parameters.

Figure 6. The collection of air temperature data.
10 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study

3. During sample collection, it is important to avoid 

grasses, stones, and pieces of debris larger than 2 millimeters (mm); if present, gently clear grasses, stones, 

and debris using gloved hands or a clean garden tool 

without removing the top layer of soil or sediment 

(fig. 8B).

4. Place a new plastic dropcloth around the sampling 

point for resting bowls and other sampling equipment 

(fig. 9A). The same plastic dropcloth may be used 

at each point as long as there is a clean place to rest 

bowls and equipment.

5. Put on a pair of nitrile gloves.

6. Collect sample for pathogens analysis.

A. Select an undisturbed area that is free from debris 

within the sample pattern.

B. Follow the “Filling Sample Containers—Pathogens” 

section.

7. Collect samples for inorganic and organic geochemistry analyses and chemistry archives.

A. Put on second pair of nitrile gloves.

B. Collect the top 2 centimeters (cm) of soil or sediment, or top 5 cm of beach sand, from each point 

within the pattern using a Teflon-coated stainless 

steel spoon, and place equal portions of soil in the 

stainless steel bowl and the plastic bowl (figs. 9B 

and 9C). The volume collected in each bowl from 

a point should be roughly proportional to 1 liter (L) 

divided by the number of subareas chosen for the 

site (for example, a transect with five composite sites 

would have about 200 mL of soil collected in each 

bowl [400 milliliters (mL) total] per point). Note: If 

excess amounts of grasses, stones, or other debris 

cannot be easily brushed aside or dissociated from 

the soil, sand, or marsh sediment, gently sieve the 

material through a stainless steel sieve (for media 

sieved into the stainless steel bowl) and a plastic 

sieve (for media sieved into the plastic bowl) each 

with a 2-mm pore size and make note of the sieve 

use in the field form “Notes” section. Keep bowls 

covered (aluminum foil for stainless steel bowl and 

plastic for plastic bowl) between subareas (fig. 9D).

A

B

Figure 8. Examples of A, sample locations at sample types, and B, sample point preparations.
Sampling Methods 11

C. Continue until all points in the pattern have been 

sampled and at least 1 L of soil has been collected in 

each bowl (fig. 9E).

D. Use Teflon-coated stainless steel spoon to gently 

homogenize sample in each bowl, taking care not to 

scrape the edge of the bowls (figs. 9F and 9G).

E. Remove outer gloves and put on new pair of nitrile 

gloves.

F. Using the Teflon-coated stainless steel spoon, fill jars 

for inorganic and organic geochemistry and chemistry archive samples per the respective subsection in 

the “Filling sample containers” section.

Sampling Bed Sediment

For bed sediment sample, two sampling personnel are 

necessary.

1. Determine which sampler to use:

A. If water depth is 4 ft or less, sampling can be 

conducted with the Ekman sampler with the handle 

attached.

B. If the water is greater than 4 ft deep, choosing 

between the Ekman and Petite Ponar samplers is 

dependent upon the substrate and the intensity of 

the waves or current. The Ekman sampler is the best 

A C

E

G

B

D F

Figure 9. Steps for collecting and homogenizing soil in stainless steel and plastic 

bowls for organic and inorganic geochemistry analysis and archives.
12 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study

choice for finely divided muck, mud, ooze, submerged marl, and fine peaty materials that are free 

from vegetation, such as sticks and decayed leaves 

(or with short, erect vegetation only) as well as intermixtures of sand, stones, and other coarse debris. 

The Ekman sampler is not recommended for rocky 

or sandy bottoms or moderate macrophyte growth 

because small pebbles or macrophyte stems prevent 

proper jaw closure. The Petite Ponar sampler is better suited for sampling compacted material, locations 

with debris (for example, sticks, pebbles, shells) and, 

because it is heavier than the Ekman sampler, locations where current/wave action is a factor. If unsure 

of the substrate, the Petite Ponar sampler should be 

used.

2. [Clean Hands] Put on a new pair of nitrile gloves.

3. [Dirty Hands] Deploy and retrieve sampler (figs. 10A 

and 10B).

A. Place sampler on clean surface and remove screens 

(Petite Ponar sampler) or open doors (Ekman sampler) to ensure that an appropriate sample was collected (fig. 10C). If a representative sample was not 

collected (for example, only shells or seaweed was 

grabbed), reset sampler and redeploy.

B. [Clean Hands] Allow sample to rest for 1 minute to 

allow flocculate to settle. Remove overlying water 

(if necessary) from sample containers using gentle 

suction with the peristaltic pump or disposable 

syringe; immerse tubing or inlet just below water 

surface so as to not come in contact with sediment 

or floc.

C. [Clean Hands] Remove the upper 2 cm with Tefloncoated stainless steel spoon and place equal amounts 

of the sediment into the stainless steel bowl and the 

plastic bowl (fig. 10D). 

A

C

B

D

Figure 10. Steps for collecting bed sediment samples using a Petite Ponar sampler.
Sampling Methods 13

D. Multiple grab samples will be required to collect the 

total amount of sediment required for all analyses, 

and it is important to not collect from the same spot 

(thus collecting the deeper sediment). Move over 

slightly to collect a grab from a different spot. 

Note: When sampling from a boat, the boat 

should be anchored at the station before attempting to sample. Drifting tends to occur (even when 

anchored) and will usually help position the sampler 

for a different grab at each drop. However, if after 

the initial grab, it is not easy to discern between 

disturbed sediment and fresh sediment (for example, 

there is no clear distinction between the oxic and 

anoxic layers after removing the top 2 cm where in 

previous samples there was), move the boat forward 

one boat length to increase probability that a sample 

is not collected at the same point.

E. Collect sample for pathogen analysis from one (or 

more, if necessary) grab: Prior to collecting for 

chemistry analyses for that grab, follow the “Filling 

Sample Containers—Pathogens” section.

4. Repeat step 3A-D until 1 L of sediment has been collected in each bowl. Note: If excessive biota or debris 

(greater than 2 mm) is present, collect additional sediment in sample containers 02, 05, 06, 07, and 08.

5. [Clean Hands] Use Teflon-coated stainless steel spoon 

to homogenize sample in each bowl.

6. [Clean Hands] Remove top gloves and put on a new 

pair of nitrile gloves.

7. Collect samples for inorganic and organic geochemistry analyses and chemistry archives.

A. Using the Teflon-coated stainless steel spoon, fill jars 

for organics and chemistry archive (for organics) 

samples per the respective subsection in the “Filling 

Sample Containers” section.

B. Using the Teflon-coated stainless steel spoon, fill jars 

for inorganics and chemistry archive (for inorganics) 

per the “Filling Sample Containers” section.

Filling Sample Containers

All soil, surficial sediment, and bed sediment collected 

from multiple subareas or grabs at a site are to be homogenized in the stainless steel bowl for organic geochemistry 

analyses and a plastic bowl for inorganic geochemistry 

analyses and distributed to the appropriate prelabeled containers for inorganic and organic screenings (with the exception of 

samples for pathogen screening, which are collected separately [without homogenization]) by scrapping the top 2 cm of 

single composite point or grab. Barcodes should be scanned 

(if device is capable) or entered manually (numbers below 

barcode) in the field. The field information will be stored in 

the database and sent along with the barcode information to all 

laboratories. The following list describes the sampling vessel 

filling procedure for each suite of analyses and also is summarized in table 2:

1. Pathogens

Note: this sample is not taken from the bowl used to 

homogenize material for organic and inorganic analyses.

A. Put on a second pair of nitrile gloves in addition to 

the base pair.

B. Using the sterile 50-mL centrifuge (container code 

01)

I. Remove the cap—DO NOT put the cap down, 

keep in hand away from other objects and out of 

the wind and precipitation.

II. Carefully skim the surface of the soil or sediment 

(with vial label pointing up) or use a sterile 

disposable plastic spatula to help scoop samples 

into vial filling the tube to at least the 40-mL mark 

(figs. 11A and 11B).

III. Tap side of vial gently to shake loose sample stuck 

on the threaded opening.

IV. Cap tightly; do not overtighten (fig. 11C).

V. Wipe vial of excess soil or sediment and moisture 

with a clean laboratory wipe.

VI. Wrap cap with precut Parafilm® (figs. 11D and 

11E).

VII. Place tube in small zip-top bag (fig. 11F).

VIII. Place in small foam shipping cooler with frozen 

gel packs to chill (fig. 11G).

C. Remove outer pair of gloves.

2. Inorganic Geochemistry

A. Inorganics sample

I. Using the Teflon-coated stainless steel spoon, 

fill the 250-mL plastic high-density polyethylene 

(HDPE) jar (container code 02) until three-fourths 

full with soil or sediment from the plastic bowl 

(fig. 12A).

II. Gently clean rim of jar with a clean laboratory 

wipe (fig. 12B).

III. Cap tightly; do not overtighten (fig. 12C).

IV. Place jar in small zip-top bag (fig. 12D).
14 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study Table 2. Sample requirements for soil and sediment collection. [Each analytical method requires specific sample containers, amount of material required, and preservation. Container code represents the two-digit suffix on the barcode labels. Maximum holding time, which is the acceptable duration of time between sample collection and shipment; anything with a holding time of less than 24 hours should be shipped the day of collection (“ship same day”) via the selected cou- rier’s overnight service; mL, milliliters; HDPE, high-density polyethylene; °C, degrees Celsius] Analytical method Sample container Con- tainer code Fill amount Field preser- vation method Storage preservation method Maximum holding time under storage Ship- ping preser- vation Destina- tion Contingency field storage Pathogens 50 mL sterile plastic centrifuge tube 01 40 mL Frozen gel packs None, ship same day 12 hours Frozen gel packs St. Petersburg, Florida Triple bag in small zip-tops; keep cold on ice in cooler Inorganic Geochemistry 250 mL plastic HDPE jar 02 3⁄4-full Chill on ice None, ship same day 48 hours Water ice Denver, Colorado Keep cold on ice in cooler or in freezer Soil Moisture 50 mL sterile plastic centrifuge tube 03 50 mL Chill on ice None, ship same day 48 hours Water ice Denver, Colorado Keep cold on ice in cooler or in freezer Methylmercury 50 mL sterile plastic centrifuge tube 04 20 mL Chill on ice Freeze at -20 °C, ship all vials when sampling complete 6 months Water ice Middleton, Wisconsin Keep cold on ice in cooler or in refridgerator Organic Geochemistry 1 250 mL baked amber jar with Teflon-lined cap 05 3⁄4-full Chill on ice None, ship same day 24 hours Water ice Lawrence, Kansas Keep cold on ice in cooler or in freezer Organic Geochemistry 2 250 mL baked amber jar with Teflon-lined cap 06 3⁄4-full Chill on ice None, ship same day 24 hours Water ice Lawrence, Kansas Keep cold on ice in cooler or in freezer Chemistry Archive (Inorganics) 250 mL plastic HDPE jar 07 3⁄4-full Chill on ice Freeze at -20 °C 6 months Water ice Lawrence, Kansas Keep cold on ice in cooler or in freezer Chemistry Archive (Organics) 125 mL baked amber jar with Teflon-lined cap 08 3⁄4-full Chill on ice Freeze at -20 °C 6 months Water ice Lawrence, Kansas Keep cold on ice in cooler or in freezer
Sampling Methods 15

B. Soil moisture sample

I. Using the Teflon-coated stainless steel spoon, fill 

the 50-mL centrifuge tube (container code 03) 

with 50 mL of soil or sediment from the plastic 

bowl (fig. 13A).

II. Gently clean rim of jar with a clean laboratory 

wipe (fig. 13B).

III. Cap tightly; do not overtighten (fig. 13C).

IV. Place vial in the same small zip-top bag as the 

inorganic screening sample jar (fig. 13D).

V. Place bag in cooler on ice to chill (fig. 13E).

C. Methylmercury sample

I. Using the Teflon-coated stainless steel spoon, fill 

the 50-mL centrifuge tube (container code 04) 

with 20 mL of soil or sediment from the plastic 

bowl (fig. 14A).

II. Clean rim of jar with a clean laboratory wipe 

(fig. 14B).

III. Cap tightly; do not overtighten (fig. 14C).

IV. Place wrapped jar in a small zip-top bag 

(fig. 14D).

V. Place bag in cooler on ice to chill (fig. 14E).

A C

E

G

B

D F

Figure 11. Steps for collecting samples for pathogens analysis (sample container 01).
16 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study

3. Organic Geochemistry

A. Using the Teflon-coated stainless steel spoon, fill two

250-mL baked amber glass jars (container codes 05 

and 06) until three-fourths full with soil or sediment 

from the stainless steel bowl (fig. 15A).

B. Clean rim of each jar with a clean laboratory wipe 

(fig. 15B).

C. Cap each jar tightly with Teflon-lined cap; do not 

overtighten (fig. 15C).

D. Wrap each jar with the large bubble-wrap protectors 

(fig. 15D).

E. Place both wrapped jars in the same large zip-top 

bag (fig. 15E).

F. Place bag in cooler on ice to chill (fig. 15F).

4. Chemistry Archive

A. Inorganics

I. Using the Teflon-coated stainless steel spoon, fill 

the 250-mL plastic (HDPE) jar (container code 

07) until three-fourths full with soil or sediment 

from the plastic bowl (fig. 16A).

II. Clean rim of jar with a clean laboratory wipe 

(fig. 16B).

III. Cap tightly; do not overtighten (fig. 16C).

IV. Place jar in a large zip-top bag (fig. 16D).

B. Organics

I. Using the Teflon-coated stainless steel spoon, fill 

the 125-mL baked amber glass jar (container code 

A

C

B

D

Figure 12. Steps for collecting samples for inorganics screening analysis (sample container 02).
Sampling Methods 17

A C

E

B

D

A C

E

B

D

Figure 13. Steps for collecting samples 

for soil moisture analysis (sample 

container 03).

Figure 14. Steps for collecting samples 

for methylmercury analysis (sample 

container 04).
18 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study

08) until three-fourths full with soil or sediment 

from the stainless steel bowl (fig. 17A).

II. Clean rim of jar with a clean laboratory wipe 

(fig. 17B).

III. Cap tightly—do not overtighten (fig. 17C).

IV. Wrap jar with small bubble-wrap protector 

(fig. 17D).

V. Place wrapped jar in the same large zip-top bag as 

the inorganics geochemistry archive jar (fig. 17E).

VI. Place bag in cooler on ice to chill (fig. 17F).

Sequential replicates are to be collected at the same time 

as the environmental sample for stations where a replicate 

(quality control) sample is planned. The purpose of collecting 

a sequential replicate sample is to identify and characterize 

the variability in the sampling process and the sample site. A 

sequential replicate is collected by filling two sets of bowls 

(plastic and stainless steel) with the predetermined volume 

from the same subareas as close to the sample points as possible before moving to the next subarea. Two sets of prelabeled 

containers are then filled (there is nothing on the labels to 

indicate a replicate, and though the use of sets with sequential 

sample-set identifiers is preferred, it is not required). The first 

sample will be stored in the database as REGULAR environmental sample (USGS National Water Information System 

[NWIS] Sample Type code 9), and the second sample will be 

stored in the database as the sequential REPLICATE (NWIS 

Sample Type code 7).

To collect a field blank for the pathogens method, follow 

the “Filling Sample Containers—Pathogens” section except

use the sterile soil provided to fill vial 01B directly, or use 

a new sterile disposable spatula. When transferring sterile 

soil, be careful not to expose the blank sample to precipitation or surfaces (other than the sterile spatula, if needed). The 

blank sample should be shipped in the same cooler as the 

environmental sample from the same site (vials will have the 

same sample-set identifier). The pathogen blank sample will 

be stored in the database as the sequential FIELD BLANK 

(NWIS Sample Type code 2).

It is important that the sample site is left minimally 

disturbed. Once sampling at a site is complete, repair divots 

in the soil (by covering or adding nearby soil) and replace any 

objects moved prior to collecting a sample. Collect all gloves, 

booties, masks, used laboratory wipes, plastic dropcloths, and 

other used disposables and trash, place it in a trash bag, and 

dispose of back at the office.

A C

E F

B

D

Figure 15. Steps for collecting samples for organics screening analysis (sample containers 05 and 06).
Sampling Methods 19

Cleaning and Sanitizing Equipment

All equipment should be thoroughly cleaned using the 

steps outlined below in a clean environment (such as a field 

preparation laboratory) and away from running vehicles or 

other sources of contamination. Thoroughly cleaning and 

sanitizing (if necessary) equipment in the field is only required 

if the same equipment is to be used for another site in the same 

outing; otherwise, equipment can be rinsed with tap water and 

cleaned in a field preparation laboratory or other appropriately 

equipped space.

1. Put on a pair of nitrile gloves.

2. Set up a clean working space using aluminum foil and 

clean laboratory wipes for resting cleaned equipment.

3. Rinse equipment (spoons, bowls, sampler, and sieves 

[if used]) with tap water.

4. Use nylon brush to remove particles; be sure to clear 

any material stuck in the moveable and removable 

parts of the sampler (for example, the screens of the 

Ponar sampler), and rinse with tap water.

5. In the field between sites, gently clean equipment 

with nylon brush and a dilute solution of LiquinoxTM

soap. Rinse thoroughly with tap water, followed by 

deionized (DI) water. Follow step 6 below for sanitization if necessary. Wrap in aluminum foil, and place in a 

bag to keep clean between sites. Upon returning to the 

office, equipment should be thoroughly cleaned and 

placed on a clean surface to air dry (away from any 

potential sources of airborne or waterborne contaminants) before wrapping in aluminum foil for storage or 

next use.

6. Sampling equipment that is not presterilized and is 

used before or during the collection of a pathogen 

Figure 16. Steps for collecting samples for inorganics chemistry archive (sample container 07).

A

C

B

D
20 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study

sample (samplers [such as the Ponar] and the stainless 

steel trowel [in the absence of a disposable sterile 

spatula]) should be sanitized at least 30 minutes prior 

to use according to the process outlined by Bowling 

and others (2014).

A. Put on a new pair of nitrile gloves.

B. Pick up one piece of equipment at a time.

C. Wipe down equipment using a 70-percent alcohol 

wipe.

D. Wipe down equipment using a 10-percent bleach 

wipe.

E. Place bleached equipment in zip-top bag (must 

remain in bag with bleach residue for at least 

30 minutes; this can be traveltime between sites).

F. After 30 minutes, put on a new pair of nitrile gloves 

to remove the equipment from the bag.

Quality Control During Sample Collection

Samples are collected in accordance with the USGS and 

EPA guidelines outlined in Radtke (2005) and Bowling and 

others (2014), each of which describes proper quality-control 

procedures during a sampling event. Procedures such as multiple glove exchanges during sampling, proper sample handling, 

and following the cleaning/sanitizing protocol emphasized 

in this SOP will minimize the potential for contamination of 

the sample by personnel and from cross contamination across 

sites. Sequential replicate samples collected in the field for 

analyses represent 10 percent of the total sample set. Sterile 

soil that is transported and transferred to a sample vial in the 

field (that is, a field blank) is used for quality control by the 

field crew collecting samples for pathogen analyses and represents 10 percent of the total sample set. Laboratory quality 

controls specific to each analytical method (such as spikes, 

blanks, and analysis of reference materials) are documented in 

respective methods documentation.

A C

E F

B

D

Figure 17. Steps for collecting samples for organics chemistry archive (sample container 08).
Sampling Methods 21

Post Sample-Collection Procedure

Uploading Field Data

Data collected in the field using electronic field forms 

(Appendix 3) are uploaded to the formhub.org server the 

same day that the overnight samples are shipped to ensure the 

chain-of-custody sequence is maintained. If a paper version 

of the field form (Appendix 4) is used, the information and 

data must be transferred/entered into an electronic field form 

as soon as possible. Data from the field form are synchronized 

with the databases in each of the USGS laboratories participating in the SCoRR study by way of the online server and a 

laboratory ODK form, which will be completed by laboratory 

staff receiving the samples. Information from the field form, 

such as field parameters, collection date and time, and field 

photographs, will be available to laboratory staff as they log in 

samples.

Shipping Samples

The foam shipping coolers supplied to field crews can 

hold two sample sets and the appropriate amount of ice (or 

frozen gel packs). Ideally, two samples would be collected 

per field trip; however, if two cannot be sampled in a day, it 

is important to note the maximum time each container can be 

stored in order to not compromise the analytical results 

(table 2 outlines the shipping requirements for each sample 

container). Before the box is sealed, a SCoRR Cooler 

Inventory Form (Appendix 5) is completed and included with 

the shipment. The cooler boxes are prelabeled with overnight 

shipping return labels, indicating the respective laboratories 

and required overnight shipping; boxes can be shipped from 

any of the contracted courier’s staffed location or using their 

pick-up service.

Figure 18 portrays the chain of custody for samples collected for the SCoRR project, and table 3 lists the shipping 

addresses for each laboratory to which samples are being 

Figure 18. Diagram showing chain of custody for samples collected for the Sediment-bound Contaminant 

Resiliency and Response (SCoRR) study. (*, If -20 °C storage at the field office is not possible, ship sample 

container 04 with containers 02 and 03 in same cooler overnight to the Colorado laboratory and the chemistry 

archive samples (containers 07 and 08) with containers 05 and 06 in same cooler overnight to the Kansas 

laboratory.)

Storage in field

Pathogens Lab

Inorganics Lab

05E1 06

Methylmercury Lab

Bioassays Lab

GC-MS/MS Lab

Archive at -20 °C Organics Lab Archive at -20 °C

Frozen gel

packs

Ship 01

with

frozen

gel packs

Ship

02 & 03

jars on

ice

Store 04

until all

assigned

sites have

been

sampled*

Ship all

04 vials

together

on ice

Ship

05 & 06

on ice

Store

07 & 08

until all

assigned

sites have

been

sampled*

Ship all archived 07 & 08

jars together on ice

Extracts from

Inorganics Lab

Extracts from

Organics Lab

All 06 jars stored (at -20 C) °

at Inorganics Lab and

shipped to contract lab for

analysis

Ice Ice Ice Ice

01 02 03 04 05 06 07 08

02E1

* *
22 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study

submitted for the 2015–16 sampling season. Samples being 

sent to the USGS pathogens laboratory in St. Petersburg, 

Florida, have a short hold time (12 hours) and must be shipped 

by overnight transport on the same day they are collected. 

When shipping these vials, use two frozen gel packs (one on 

top and one on bottom), insert foam cover, close box, and tape 

seams with packing tape (fig. 19A). In the event, gel packs 

cannot be kept frozen (for example, multiple-day field trips 

without access to a freezer), ice may be placed in a large ziptop bag, bagged again, and placed on top of the double-bagged 

sample vial(s) for shipping. 

Samples being sent to the USGS laboratories in Denver, 

Colorado, and Lawrence, Kansas, for inorganic and organic 

geochemistry analyses, respectively, should be shipped by 

overnight transport on the same day of collection but may be 

stored at -20 degrees Celsius (°C) for up to 24 hours if additional samples are to be collected and shipped together the following day. When shipping these containers, line the inside of 

the large foam shipping coolers with a plastic bag, place jars 

in the appropriate box (sets of containers 02 and 03 should be 

in the same bag and are shipped together to Denver, Colorado; 

sets of containers 05 and 06 should be shipped together to 

Lawrence, Kansas), fill with ice to just below cooler edge, tie 

off the bag, insert foam cover (the lid must be closed completely and fit snug), close box, and tape seams with packing 

tape (fig. 19B). 

Should shipment be delayed and a freezer is not available, it will be necessary to fill the standard cooler being used 

to transport the samples with ice. Samples collected for inorganic and organic geochemistry analyses, as well as chemistry 

archives, are to be kept in a cooler with an abundance of ice or 

stored in a freezer set to a constant temperature of at least -20 

°C until they can be shipped (except for soil moisture sample 

vial (container 03), which can be kept in refrigerator or on 

ice). For samples collected for pathogen analyses, vials should 

be triple-bagged with zip-top bags and kept completely surrounded by ice; DO NOT freeze pathogens vial (container 01).

All sample containers labeled 06 will be stored at -20 °C 

at the organics laboratory until sampling is complete, at which 

time the jars will be forwarded to a contracted laboratory 

for gas chromatography tandem mass spectroscopy analyses 

(GC–MS/MS) (fig. 18). Samples collected for methylmercury 

analysis (container 04) at the USGS Middleton, Wisconsin, 

laboratory are to be stored at -20 °C until all sampling has 

Table 3. Shipping destinations and preservation for samples collected under the Sediment-bound Contaminant Resiliency and 

Response (SCoRR) study.

[ml, milliliters; HDPE, High-density polyethylene]

Analytical method Sample container Container code Destination

Pathogens 50 milliliter (mL) sterile plastic centrifuge tube 01

Dale Griffin

U.S. Geological Survey

600 4th Street South

St. Petersburg, FL 33701

Inorganics

250 mL plastic HDPE jar

50 mL sterile plastic centrifuge tube

02

03

William Benzel

U.S. Geological Survey

Denver Federal Center

Bldg. 810, ENT E-11, MS-973

Denver, CO 80225

Methylmercury 50 mL sterile plastic centrifuge tube 04

U.S. Geological Survey

Methylmercury Research Laboratory

8505 Research Way

Middleton, WI 53562

Organics

250 mL baked amber jar with Teflon-lined cap

250 mL baked amber jar with Teflon-lined cap

05

06

Keith Loftin

U.S. Geological Survey

Organic Geochemistry Research Lab

4821 Quail Crest Place

Lawrence, KS 66049

Chemistry archive

250 mL plastic HDPE jar

125 mL baked amber jar with Teflon-lined cap

07

08

Keith Loftin

U.S. Geological Survey

Organic Geochemistry Research Lab

4821 Quail Crest Place

Lawrence, KS 66049
Sampling Methods 23

A

B

Figure 19. Examples of foam shipping coolers packed to efficiently utilize space and minimize breakage for 

A, pathogen samples, and B, organic geochemistry samples (use the same method for inorganic geochemistry 

samples [not shown]).
24 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study

been completed by the field office. The vials should then 

be shipped, on ice, in a single cooler by overnight transport 

along with an inventory form found on the laboratory website 

(http://wi.water.usgs.gov/mercury-lab/forms.html). Similarly, 

samples collected for chemistry archive (containers 07 and 

08) should be stored at -20 °C until all sampling has been 

completed by the field office, then the jars can be packed in 

coolers, on ice, and shipped to the USGS organics laboratory 

in Lawrence, Kansas, by overnight transportation. If -20 °C 

storage at the field office is not possible, ship sample container 

04 with containers 02 and 03 in same cooler overnight to the 

Colorado laboratory and the chemistry archive samples 

(containers 07 and 08) with containers 05 and 06 in same 

cooler overnight to the Kansas laboratory. Including the 

additional containers will result in only having room for one 

sample set per foam shipping cooler.

Selected References

Anderson, J.R., Hardy, E.E., Roach, J.T., and Witmer, R.E., 

1976, A land use and land cover classification system 

for use with remote sensor data: U.S. Geological Survey 

Professional Paper 964, 28 p. [Also available at http://pubs.

er.usgs.gov/publication/pp964.]

Bowling, C.Y., Griffin, D.W., Mattorano, Dino, Silvestri, Erin, 

Schaefer, F.W., and Nichols, T.L., 2014, USEPA/USGS 

sample collection protocol for bacterial Protection Agency, 

EPA/600/R–14/027, 40 p.

Buxton, H.T., Andersen, M.E., Focazio, M.J., Haines, J.W., 

Hainly, R.A., Hippe, D.J., and Sugarbaker, L.J., 2013, 

Meeting the science needs of the Nation in the wake of 

Hurricane Sandy—A U.S. Geological Survey science plan 

for support of restoration and recovery: U.S. Geological 

Survey Circular 1390, 26 p. [Also available at http://pubs.

usgs.gov/circ/1390/.]

Ciparis, Serena, Iwanowicz. L.R., and Voshell, J.R. 2012, 

Effects of watershed densities of animal feeding operations 

on nutrient concentrations and estrogenic activity in agricultural streams: Science of the Total Environment, v. 414, 

p. 268–276.

Fischer, J.M., Phillips, P.J., Reilly, T.J., Focazio, M.J., Loftin, 

K.A., Benzel, W.M., Jones, D.K., Smalling, K.L., Fisher, 

S.C., Fisher, I.J., Iwanowicz, L.R., Romanok, K.M., 

Jenkins, Darkus, Bowers, L., Boehlke, Adam, Foreman, 

W.T., Deetz, A.C., Carper, L.G., Imbrigiotta, T.E., and 

Birdwell, Justin, 2015, Estuarine bed-sediment-quality 

data collected in New Jersey and New York after Hurricane 

Sandy, 2013: U.S. Geological Survey Data Series 905, 

42 p., plus CD-ROM. [Also available at http://dx.doi.

org/10.3133/ds905.]

Griffin, D.W., Silvestri, Erin, Bowling, C.Y., Boe, T., Smith, 

D.B., and Nichols, T.L. 2014, Anthrax and the geochemistry 

of soils in the contiguous United States: Geosciences, v. 4, 

no. 33, p. 114–127.

Hoefen, T.M., Kokaly, R.F., Martin, D.A., Rochester, Carlton, 

Plumlee, G.S., Mendez, Greg, Reichard, E.G., and Fisher, 

R.N., 2009, Sample collection of ash and burned soils 

from the October 2007 southern California wildfires: U.S. 

Geological Survey Open-File Report 2009–1038, 64 p.

Knapen, D., Reynders, H., Bervoets, L., Verheyen, E., and 

Blust, R., 2007, Metallothionein gene and protein expression as a biomarker for metal pollution in natural gudgeon 

populations: Aquatic Toxicology, v. 82, no. 3, p. 163–172.

Lane, S.L., and Fay, R.G., 1997, Safety in field activities: 

U.S. Geological Survey Techniques of Water-Resources 

Investigations, book 9, chap. A9, October 1997, accessed 

April 6, 2015, at http://pubs.water.usgs.gov/twri9A9/. 

Plumlee, G.S., Morman, S.A., Meeker, G.P., Hoefen, T.M., 

Hageman, P.L., and Wolf, R.E., 2014, The environmental 

and medical geochemistry of potentially hazardous materials produced by disasters: Elsevier, chap. 11.7, p. 257–304.

Radtke, D.B., 2005, Bottom-material samples (ver.1.1): 

U.S. Geological Survey, Techniques of Water-Resources 

Investigations, book 9, chap. A8, accessed July 15, 2015, at 

http://pubs.water.usgs.gov/twri9A8/. 

Reilly, T.J., Jones, D.K., Focazio, M.J., Aquino, K.C., Carbo, 

C.L., Kaufhold, E.E., Zinecker, E.K., Benzel, W.M., Fisher, 

S.C., Griffin, D.W., Iwanowicz, L.R., Loftin, K.A., and 

Schill, W.B., 2015, Strategy to evaluate persistent contaminant hazards resulting from sea-level rise and stormderived disturbances—Study design and methodology for 

station prioritization: U.S. Geological Survey Open-File 

Report 2015–1188A, 20 p., http://dx.doi.org/10.3133/

ofr20151188A.

Shelton, L.R., and Capel, P.D., 1994, Guidelines for collecting and processing samples of stream bed and sediment 

for analysis of trace elements and organic contaminants 

for the National Water-Quality Assessment Program: U.S. 

Geological Survey Open-File Report 94–458. [Also available at http://water.usgs.gov/nawqa/pnsp/pubs/ofr94-458/.]

Silvestri, E., Brady-Roberts, E., Sherman, R., Schaefer, F., and 

Griffin, D. 2014, Quality assurance project plan category 

4, QAPP# TCAD B.1.1.4, Analyses of Bacillus anthracis 

spores from soil: U.S. Environmental Protection Agency, 

Threat Consequence Assessment Division, National 

Homeland Security Research Center, Cincinnati, Ohio and 

U.S. Geological Survey, Contaminant Biology Program, St. 

Petersburg, Florida.
Selected References 25

Stavreva, D.A., Klausmeyer, P., George, A.A., Varticovski, L., 

Sack, D., Voss, T.T., Schiltz, R.L., Blazer, V.V., Iwanowicz, 

L.R., and Hager, G.L, 2012, Prevalent glucocorticoid and 

androgen activity in US water sources: Scientific Reports, 

v. 2, no. 937. 

U.S. Department of Agriculture, Soil Survey Program, Natural 

Resources Conservation Service, Technical soil services 

handbook, accessed July 15, 2015, at http://www.nrcs.usda.

gov/wps/portal/nrcs/detail/soils/survey/publication/?cid=nrc

s142p2_053400.

U.S. Department of Agriculture, Regulated Organism 

and Soil Program, accessed June 10, 2015, at http://

www.aphis.usda.gov/wps/portal/aphis/ourfocus/

planthealth/sa_import/sa_permits/sa_plant_pests/!ut/p/

a1/jZDNDoIwEISfyHRt-JEjBYQCVS9E7IX-

0oNgESgONB59ewLOVPc1uvtnNLOKoRlyJl2yF-

kYMS3dJzr8nPGd4TwDRNEwL0dCwvfpFjYO4M3Cx-

A4W7zR2mYOX4JAM4BA41JFvsBA6DeNj_8qBD—

fMNB_DIItYiroV57qR6DKieRCN7PYxmlfo9tJMX90JZebJNPdXxK3rl_esgC3_ClgC6r6q6ndJAirDD9-

NWJ8!/?1dmy&urile=wcm%3apath%3a%2Fap

his_content_library%2Fsa_our_focus%2Fsa_plant_

health%2Fsa_import%2Fsa_permits%2Fsa_plant_

pests%2Fsa_soil%2Fct_regulated_organism_soil_permits_

home.

U.S. Geological Survey, variously dated [a], Occupational 

safety and health program requirements handbook: U.S. 

Geological Survey Manual, SM 445–2–H, accessed July 

15, 2015, at http://www.usgs.gov/usgs-manual/handbook/

hb/445-2-h.html.

U.S. Geological Survey, variously dated [b], National 

field manual for the collection of water-quality data: 

U.S. Geological Survey Techniques of Water-Resources 

Investigations, book 9, chaps. A1–A9, available online at 

http://pubs.water.usgs.gov/twri9A.

U.S. Geological Survey, 2006, Collection of water samples 

(ver. 2.0): U.S. Geological Survey Techniques of WaterResources Investigations, book 9, chap. A4, September 

2006, accessed April 6, 2015, at http://pubs.water.usgs.gov/

twri9A4/.

Wilde, F.D., ed., variously dated, Field measurements: 

U.S. Geological Survey Techniques of Water-Resources 

Investigations, book 9, chap. A6, with sec. 6.0–6.8, accessed 

April 6, 2015, at http://pubs.water.usgs.gov/twri9A6/.

Glossary 27

Bed sediment Sediment covered by water 

(referred to as bottom material in USGS 

National Field Manual).

Composite A sample made up of multiple 

grab samples from subareas.

HomogenizeTo mix thoroughly such that 

all media from composites are uniformly 

distributed.

Site An area around the station from which 

samples are collected using determined sam-

pling pattern.

Station

A specific GPS location. Stations 

are given unique station identification num-

bers and are the reference location for the 

sample site.

Subarea The divided area based on a 

sample pattern from which a single composite 

sample will be collected.

Surficial sediment Sediment exposed to 

the atmosphere (not covered by water), for 

example, beach sand.

Glossary

Appendixes 1–5 29

Appendixes 1–5
30 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study

39

Appendix 1. SCoRR Standard Operating Procedure quick reference guide

Field Measurements

• Prior to sampling, position crew at desired coordinates to complete electronic field form. 

o Multi-parameter QW: Water temp., SC, pH, DO mg/L, DO %-saturation, Turbidity. 

o NIST Certified Thermistor: Soil Temperature (if applicable), Air Temperature.

o Depth to bottom (if applicable).

o Alternate coordinates, if necessary, or if proposed coordinates are incorrect. 

o Note weather: wind, precipitation, cloud cover, and other environmental conditions near sampling site.

o Include a minimum of three photos of the site/sampling location.

Media Parameter Units USGS parameter code Reference figure

Soil or sediment Soil temperature °C -- Figure 5

Air

Air temperature

Weather

Sky

Winds

°C

--

--

--

00020

--

--

--

Figure 6

Water 

(at sample depth)

Depth to bottom

Water temperature

Specific conductance

pH

Dissolved oxygen

ft

°C

μS/cm

pH units

mg/L

81903

00010

00095

00400

00300

Figure 7

Sampling Pattern Options

 GRID SPOKE TRANSECT

Sample Collection

• Soil or Surficial Sediment

o Identify the desired area of sampling making sure not to disrupt or destroy the immediate area.

o Avoid grasses, stones, and debris. If present, carefully remove with gloved hands or with a clean garden 

tool without removing top layer of soil or sediment. 

o Sample for pathogens at first station of composite sample.

o Only sample top 2 cm of soil or sediment and top 5 cm of sand.

o If large particulates and debris cannot be easily removed, use 2mm pore size sieves.

 Stainless steel sieve for stainless bowl, plastic sieve for plastic bowl.

o Continue at each composite station until 1 L of soil is collected per homogenizing bowl.

o Follow Filling Containers protocol to complete sample collection.

Appendix 1. SCoRR Standard Operating Procedure quick reference guide

Media Parameter Units USGS parameter code Reference figure

Soil or sediment Soil temperature °C -- Figure 5

Air

Air temperature

Weather

Sky

Winds

°C

--

--

--

00020

--

--

--

Figure 6

Water 

(at sample depth)

Depth to bottom

Water temperature

Specific conductance

pH

Dissolved oxygen

ft

°C

μS/cm

pH units

mg/L

81903

00010

00095

00400

00300

Figure 7

EXPLANATION

Sample site for

composite

Station

EXPLANATION

Sample site for

composite

Station

EXPLANATION

Sample site for

composite

Station
Appendix 1. SCoRR Standard Operating Procedure quick reference guide 31

40

• Bed Sediment

o Determine whether to use an Ekman (<4’ - fine sediment) or Petite Ponar (>4’ - coarse sediment); if 

unknown, Petite Ponar should be used.

 CH = Clean Hands, DH = Dirty Hands.

o DH: Deploy and retrieve sampler

o CH: Allow flocculent to settle for one minute. Remove overlying water, if necessary.

o CH: Collect pathogens on first grab; collect from additional grabs if more substrate is needed. The 

remainder of the top 2 cm/5 cm, depending on material type, of grab can be distributed to homogenizing 

bowls.

o DH: Continue to collect grabs from different locations to avoid re-sampling. 

o CH: Remove upper 2 cm for sediment or 5 cm of sand of each grab with Teflon-coated stainless steel

spoon until there is 1 L of sediment in each bowl.

o Follow Filling Containers protocol to complete sample collection. 

Filling Containers

1. Pathogens (01=Pathogens)

a. 01: Skim 50 mL centrifuge to at least 40 mL from single grab

i. Use disposable plastic spatula

ii. Clean vial and wrap in Parafilm®

iii. Small zip-top bag  Small foam shipping cooler, Frozen gel packs

2. Inorganic Geochemistry (02=Screening, 03=Soil Moisture, 04=Methylmercury)

a. 02: Fill 250 mL HDPE jar until 3⁄4-full from PLASTIC BOWL

i. Fill using Teflon coated stainless steel spoon

ii. Clean rim, close jar

iii. Large zip-top bag

b. 03: Fill 50 mL centrifuge full from PLASTIC BOWL

i. Fill using Teflon coated stainless steel spoon

ii. Clean rim, close vial

iii. Same zip-lock bag as 02  Cooler chill

c. 04: Fill 50 mL centrifuge to 20 mL from PLASTIC BOWL

i. Fill using Teflon coated stainless steel spoon

ii. Clean rim, close vial

iii. Small zip-top  Cooler, Ice

3. Organic Geochemistry (05 & 06=Organic Geochemistry)

a. 05 & 06: Fill two 250 mL amber glass jars 3⁄4-full from STAINLESS STEEL BOWL

i. Fill using Teflon coated stainless steel spoon

ii. Clean rims, close jars

iii. Place each jar with bubble-wrap sleeve

iv. Both jars in same large zip-top  Cooler, Ice

4. Chemistry Archive (07=Inorganics, 08=Organics)

a. 07: Fill 250mL HDPE jar 3⁄4-full from PLASTIC BOWL

i. Fill using Teflon coated stainless steel spoon

ii. Clean rim, close jar

iii. Large zip-top bag w/ 08  Cooler, Ice

b. 08: Fill 125mL amber glass jar 3⁄4 from STAINLESS STEEL BOWL
32 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study

41

i. Fill using Teflon coated stainless steel spoon

ii. Clean rim, close jar

iii. Place in bubble-wrap sleeve

iv. Same zip-top bag as 07  Cooler, Ice

Cleaning and Sanitizing Equipment

• Rinse all equipment at site with tap water to loosen large debris and put in plastic bag to be cleaned later at 

controlled laboratory environment. 

• Wearing nitrile gloves, set up a clean working space using aluminum foil and clean laboratory wipes. 

• Rinse all equipment (spoons, bowls, sampler, and sieves) with Tap water.

• Using a nylon brush, tap water, and dilute LiquinoxTM, gently clean surfaces of residual material.

• Rinse with tap water  Rinse with DIW  Wrap in aluminum foil and into a plastic bag to dry.

• Full sanitization is only needed for equipment in contact with soil/sediment used to collect a sample for pathogen 

analysis and should occur prior to use at the office or in the field between sites. 

o Once dry, Wipe all surfaces with 70% Alcohol Wipe  Wipe all surfaces with 10% Bleach Wipe. 

o Put equipment in bag with bleach residue (dampness) for at least 30 minutes. 

o Remove from bag just prior to use.

Uploading Field Data

• All field data are to be uploaded the same day as sample collection.

o Data needs to be available to laboratories while logging samples into the database.

 This includes field measurements, photos, and any updated information regarding the sample 

collection or sampling location.

• Upload data directly to the formhub.org Server.

Shipping

• Used supplied foam shipping containers and appropriate method of chilling/preservation; ice vs. frozen gel.

• *Be aware of sample holding times!!! Pathogens with 12-hour maximum holding time.

Analytical Method Sample Container Container 

Code Destination Maximum 

Holding Time

Shipping 

Preservation

Pathogens 50 mL sterile plastic centrifuge tube 01 St. Petersburg, FL 12 hours Frozen gel packs

Inorganics 250 mL plastic HDPE jar

50 mL sterile plastic centrifuge tube

02

03 Denver, CO 48 hours

24 hours Water ice

Methylmercury 50 mL sterile plastic centrifuge tube 04 Middleton, WI 6 months Water ice

Organics 250 mL baked amber jar with Teflon-lined cap

250 mL baked amber jar with Teflon-lined cap

05

06 Lawrence, KS 24 hours Water ice

Chemistry 

Archive

250 mL plastic HDPE jar

125 mL baked amber jar with Teflon-lined cap

07

08 Lawrence, KS 6 months Water ice
Appendix 1. SCoRR Standard Operating Procedure quick reference guide 33

42

o 01  St. Petersburg, FL ship on frozen gel packs day of sampling.

o 02, 03  Denver, CO ship on ice together day of sampling.

o 04  Middleton, WI stored together at -20o

C until sampling complete.

o 05, 06  Lawrence, KS ship on ice together day of sampling.

o 07, 08  Lawrence, KS stored together at -20o

C until sampling complete.

• Ideally sample two sites per field day. If additional day needed to submit two samples together, preserve samples 

in ice/freezer depending on sample’s needs, and ship both sites’ samples together the following day. Do not 

freeze pathogens (01) vial—triple-bag in additional zip-top bags and keep on ice or in refrigerator until next day.

• Foam shipping boxes are pre-labeled (with contracted courier labels) to respective laboratories; be sure that 

containers are placed in the proper shipping boxes.

• Line inside of large foam shipping coolers with plastic bag, small layer of ice on bottom, then bagged samples, then 

more ice to fill bag while allowing the coolers to shut snugly. Tie off plastic liner. 

• Include a SCoRR Cooler Inventory Form (app. 5) in each cooler to be sent.

• Close cooler lid and seal foam coolers with packing tape along entire seal of cooler lid.

• Seal cooler box and drop off or pick-up from any staffed or scheduled contracted courier location.

Storage in field

Pathogens Lab

Inorganics Lab

05E1 06

Methylmercury Lab

Bioassays Lab

GC-MS/MS Lab

Archive at -20 °C Organics Lab Archive at -20 °C

Frozen gel

packs

Ship 01

with

frozen

gel packs

Ship

02 & 03

jars on

ice

Store 04

until all

assigned

sites have

been

sampled*

Ship all

04 vials

together

on ice

Ship

05 & 06

on ice

Store

07 & 08

until all

assigned

sites have

been

sampled*

Ship all archived 07 & 08

jars together on ice

Extracts from

Inorganics Lab

Extracts from

Organics Lab

All 06 jars stored (at -20 C) °

at Inorganics Lab and

shipped to contract lab for

analysis

Ice Ice Ice Ice

01 02 03 04 05 06 07 08

02E1

* *
34 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study

Appendix 2. Equipment and Supplies Checklist

43

Appendix 2. Equipment and Supplies Checklist

All field kits should include the following items (at a minimum):

Personal Protection Field Equipment for bed sediment sampling

□ Nitrile gloves, non-powdered □ Standard Ekman benthic grab sampler assembly

□ Eye protection [goggles or glasses] □ (2) Messengers [1 + 1 spare]

□ Dust masks □ Handle

□ Ear plugs □ Spare trip head

□ Disposable shoe covers [booties] □ Spare cable assembly (pair)

□ Waders □ Spare spring hubs (pair)

□ Personal floatation device □ Petite Ponar benthic grab sampler assembly

□ (2) Messengers [1 + 1 spare]

Sample-Collection Supplies [per site] □ Carabiner

□ (1) Teflon-coated stainless spoons □ (2) Spare release pins

□ (1) Stainless steel trowel, thin blade □ Spare screens (pair)

□ (1) Sterile spatula [disposable] □ Braided line [double the length of the deepest site]

□ Stainless steel bowl [with 2-liter capacity or larger] □ Battery-operated peristaltic pump with tubing

□ Plastic bowl [with 2-liter capacity or larger] □ Disposable syringe (at least 60 mL)

□ (2) 250 mL wide-mouth HDPE jars

□ (2) 250 mL baked amber glass jars, Teflon-lined cap Field Supplies

□ (1) 125 mL baked amber glass jars, Teflon-lined cap □ Zip-top bags, small [roughly 6 in. x 6 in.]

□ (3) 50 mL sterile plastic centrifuge tube □ Zip-top bags, large [roughly 11 in. x 11 in.]

□ Spare set of the 8 sample containers □ (1) Bubble wrap sleeve, small [for 125 mL jar]

□ Spare set of the sample containers labels □ (2) Bubble wrap sleeve, large [for 250 mL jars]

□ Plastic drop cloth

Field Equipment □ Nylon brush [for cleaning]

□ Field device [Garmin MonterraTM] □ Carboy of deionized (DI) water

with built-in camera, satellite-based GPS, and the □ Squeeze bottle for DI water

SCoRR electronic field form preloaded □ Carboy of tap water

□ Thermometer [for air temp] □ Alcohol wipes [70% ethanol]

□ Soil thermometer [NIST calibrated] □ Bleach wipes [10%]

□ Handheld GPS [if not built into field device] □ Parafilm® strips [1.5 in. x 3 in.]

□ Digital camera [if not built into field device] □ Solution of LiquinoxTM [0.2% by volume max]

□ Paper field forms (for back-up) [Appendix 3] □ Aluminum foil [wide enough to cover bowl]

□ Engineers ruler □ Waterproof pens

□ Tape measure [25 ft. or greater] □ Laboratory wipes

□ Measuring wheel □ Cooler, large with ice

□ Stainless steel sieve [2 mm pore size] □ Sterile soil for blanks

□ Plastic sieve [2 mm pore size] □ Trash bags

□ Multiparameter water-quality sonde [YSI 6-series or 

comparable] equipped with DO, Temp/Cond, and Shipping Supplies [per site]

pH sensors for samples overlain by water □ (3) Shipping Forms, printed (Appendix 4)

□ (2) Foam shipping coolers, large

□ (2) Plastic coolers bags [for large foam coolers] 

□ Foam shipping cooler, small

□ (2) Frozen gel packs

□ Packing tape

**ALWAYS BRING A SPARE SET OF SAMPLE CONTAINERS IN THE FIELD**
Appendix 3. SCoRR Field Form—electronic version template 35

Appendix 3. SCoRR Field Form—electronic version template

44

Appendix 3. SCoRR Field Form—electronic version template

[Electronic field form created using Open Data Kit (https://opendatakit.org/) and installed on the Android-based Garmin 

MonterraTM.]

State Preloaded, select from drop-down

SCoRR ID Preloaded, select from drop-down

Station Name Preloaded, loads when SCoRR ID is selected (NWIS or stakeholder Site Name)

Station ID Preloaded, loads when Station Name is selected (NWIS IDs [if applicable])

Contact info for site access/permission Preloaded and displayed along with Station ID and Station Name based on 

selected station

Sampling Mode Choose from Resiliency, Response

Field Team Leader Pre-loaded, select from drop-down with list of WSC project field coordinators

Sampling Personnel (initials) Text box for initials those in the sampling party

Latitude Acquired automatically from built-in GPS—standardize; Decimal Degrees

Longitude Acquired automatically from built-in GPS—standardize; Decimal Degrees

GPS Accuracy Acquired automatically from built-in GPS—in feet

GPS Datum Acquired automatically from built-in GPS—should be set to NAD83

Observed Land Use in Vicinity Entered via drop-down per the Anderson Land-use classification system

Sample Location description Enter at first visit—subsequently loads when Station Name is selected

Photo(s) Tap box to activate built-in camera. Require 2: close up of a sample point with 

reference ruler, and a general location pic. Allow up to 3 more field photos per 

site.

Sample Medium Choose from Soil, Sediment—have another field in database automatically 

populated with NWIS Sample Medium codes (SO or SB)

Sample Collection Method Choose from Grid, Transect, Spoke, Boat grabs

--if Method = Grid Prompt for Individual Grid Size (sq. ft.) and Grid Length (ft.)—Range limit 

“300” for length

--if Method = Transect Prompt for Distance between Sampling Points (ft.)—Range limit “50”

--if Method = Spoke Prompt for Distance from Centroid (ft.)—Range limit “150”

--if Method = Boat grabs Prompt for Sample Area Covered (sq. ft.)

Number of Subsamples Collected for Composite Range limit “>0”

QC at site? Choose from None, Replicate—have another field in database automatically 

populated with NWIS Sample Type codes (9 or 7). If QC at site = Y, duplicate 

record in database but use Sample Medium code SOQ or SBQ

Air Temperature (°C) [00020] Range limit “-20–50”

Soil Temperature (°C) Range limit “-10–50”

Weather Choose from Clear, Rain, Fog, Snow, Sleet

Sky Choose from Sunny, Partly Cloudy, Overcast

Wind Choose from Calm, Breezy, Windy

Surface water overlaying sample? Choose from Y/N [“Y” adds 6 required fields indicated by +]

+ Depth to bottom (ft.) [81903] Range limit “lower limit 0”

+ Water Temperature (°C) [00010] Range limit “-10 to 50”

+ Specific Conductance (μS/cm) [00095] Range limit “0–50000”

+ pH [00400] Range limit “1–14”

+ Dissolved oxygen (mg/L) [00300] Range limit “0–20”

+ Sediment Sampler Type Choose from Ponar, Ekman, other

Sample Container ID number Scan or type-in each bottle ID(s) before filling in field with option to enter 

manually; Two sets of numbers to denote site and analyses (error will display if 

bottle Serial numbers don’t match); Example: XXXXX–01, XXXXX–02 where 

‘XXXXX” is the sample suite’s Serial number and container 01, etc. is the 

analyses code (01 = Pathogens, 02 = Inorganic Geochemistry, etc.)

Sample Date Acquired automatically from computer when Containers are scanned

Sample Time Acquired automatically from computer

Field Notes Text box to enter field notes—entry not required

Date and Time Field Form uploaded Acquired automatically from computer when finalized and uploaded to server
36 Standard Operating Procedure for the Collection of Soil and Sediment Samples for the SCoRR Strategy Pilot Study

Appendix 4. SCoRR Field Form—manual entry template

45

Appendix 4. SCoRR Field Form—manual entry template

U.S. GEOLOGICAL SURVEY

Sediment-bound Contaminant Resiliency and Response (SCoRR)

Field Form—Manual Entry

**PLEASE COMPLETE ENTIRE FORM**

Station Name _______________________________________________________________________________

Station ID _______________________________ Location ________________________________________

Latitude ___________________ Longitude _________________ GPS accuracy (ft.) ______________

GPS Datum ______________ Observed Land Use (circle one): Undevel. Ag. Res. Comm. Ind.

Observed Land Use Density (circle one): None H M L Sampling Personnel _________________

Sample Date _________________ Sample Time ____________ (“Standard” time—account for Daylight Savings)

Sample Medium (circle one): Soil Sand Bed Sed. Marsh Sed. Total Sample Area (sq. ft.) ________

Sample Method (circle one): Grid Transect Spoke Grab Other Number of Subsamples ___________

QC at site? None Replicate Field Spike Sampling Mode: Resiliency Response

Physical Parameters

Air Temperature (°C) [00020] __________________ Weather (circle one): Dry Rain Fog Snow

Sky (circle one): Clear Partly cloudy Overcast Winds (circle one): Calm Breezy Windy 

If water overlays sample, collect water parameters: For Soil, Sand, and Marsh Sediment samples:

Depth to bottom (ft.) [81903] ____________ Soil Temperature (°C) ______________

Water Temperature (°C) [00010] ____________

Specific Conductance (μS/cm) [00095] ____________ For Bed Sediment samples:

pH [00400] ____________ Sediment Sampler Make/Model ______________

Dissolved oxygen (mg/L) [00300] ____________ Sediment Sampler Type ______________

Sample Container ID ________________-XX Filled: □ 01 | □ 02 | □ 03 | □ 04 | □ 05 | □ 06 | □ 07 | □ 08

Photo(s) file name ___________________________________________________________________________

Field Notes _________________________________________________________________________________

___________________________________________________________________________________________

**Transpose this form into the SCoRR Electronic Field Form application as soon as possible (and retain for records)**
Appendix 5. SCoRR Cooler Inventory Form 37

Appendix 5. SCoRR Cooler Inventory Form

46

Appendix 5. SCoRR Cooler Inventory Form

Contents of Shipping Cooler

USGS Sediment-bound Contaminant Resiliency and Response (SCoRR) Pilot Study

Select Lab/Contact:

□ Pathogens | Dale Griffin □ Inorganics | William Benzel □ Organics | Keith Loftin □ Archives | Keith Loftin

Sample-set

Identifier

Container(s) 

Identifier

SCORR ID Sample Date

(yyyymmdd)

Sample Time

(hhmm)

Soil 

Temperature, 

field (°C)

Shipped with

ex: NY-999999 02 & 03 NY-03246 20150701 1300 21.0 ice

Chain of Custody

WSC Point of Contact: _____________________________________ phone: __________________ email: __________________________

Sampling Personnel: ________________________________________________________________________

Signature: ______________________________________ Date Shipped: _________________________

Lab log-in: ___________________________________________ phone: __________________ email: __________________________

Signature: ______________________________________ Date Received: _________________________

Version 1 (2015)

For additional information:

U.S. Geological Survey

Toxic Substances Hydrology Program

12201 Sunrise Valley Drive

Reston, Virginia 20192

Or visit the U.S. Geological Survey Environmental Health Web site at:

 http://www.usgs.gov/envirohealth/

Document prepared by the West Trenton Publishing Service Center
Fisher and others—Standard Operating Procedure for Collection of Soil and Sediment Samples for the Sediment-bound Contaminant Resiliency and Response 

(SCoRR) Strategy Pilot Study—Open-File Report 2015–1188B

ISSN 2331-1258 (online)

http://dx.doi.org/10.3133/OFR20151188B