1

Research Note RMRS-RN-49. 2012

Sampling Procedure for Lake or Stream 

Surface Water Chemistry

Robert Musselman

Rocky Mountain Research Station

Research Note

United States Department of Agriculture

Forest Service

Rocky Mountain Research Station

Research Note RMRS-RN-49

May 2012

Citation:

Musselman, Robert. 2012. Sampling procedure for lake or stream surface 

water chemistry. Res. Note RMRS-RN-49. Fort Collins, CO: U.S. Department of 

Agriculture, Forest Service, Rocky Mountain Research Station. 11 p.

Introduction

Surface waters collected in the field for chemical analyses are easily 

contaminated. This research note presents a step-by-step detailed 

description of how to avoid sample contamination when field collecting, 

processing, and transporting surface water samples for laboratory 

analysis.

Locate Sample Collection Site

Choose a sampling spot with fast-moving water, at least 15-20 cm 

(6-8 inches) deep if possible, and where you can reach it from a solid 

place on the stream bank (rocky, not soft/spongy spot) or from a 

large rock. Streams are always sampled upstream from any bridge, 

culvert, flume, or other artificial structure. Lakes are sampled at their 
2

Research Note RMRS-RN-49. 2012

outlet unless the chemistry of the lake profile is needed. Approach 

the sampling location from downstream if possible. If collections are 

repeated over time, check the previous collection field notes for exact 

sampling location and collect from the same sampling site. A GPS 

identification of the location is helpful.

Take Water Temperature

Place thermometer in the water near the sampling point, preferably 

downstream. Avoid disturbing the bottom at the sample site. Allow 

the thermometer to equilibrate (reach stream temperature and stop 

changing) and record the temperature. It may take a couple of minutes 

to equilibrate. Digital thermometers equilibrate faster and are easier to 

determine when they have reached water temperature.

Label Bottle Correctly

Sample bottles should be brown 250 ml (about 1 cup volume) highdensity polyethylene (HDPE) or low-density polyethylene (LDPE) 

plastic unless otherwise instructed. Before immersion of the sample 

bottle, use a black permanent marker to write on the dry bottle the 

sample location (geographic area name and stream or lake name), date 

and year, time of day (indicate daylight or standard time as MDT or 

MST), water temperature (add oF or oC), and sampler’s first and last 

name.

Avoid Contaminating Bottle

After the bottle is labeled, put on the gloves (latex or nitrile, and 

powder-free) and rinse the capped bottle and the gloves downstream to 

remove any possible contaminants. Be careful not to touch your face, 

the ground, or anything except the bottle after the gloves and bottle are 

rinsed. Fingers contain contaminants such as nitrates. Insect repellents, 

sunscreen, and cigarette smoke are particularly troublesome as 

contaminants. Do not touch anything except the sample bottle once the 

gloves are on. Avoid glove and sample contact with the ground or with 

human skin or clothing, and avoid breathing directly in/on the bottle or 

cap during sample collection.
3

Research Note RMRS-RN-49. 2012

Prepare Bottle for Sampling

First rinse the inside of the bottle, the inside of the cap, and the rim 

with the deionized water (DIW) that comes in the bottle. To rinse, 

remove the cap with index finger and thumb, palm facing up (Figures 

1-2). If the cap is not held correctly when removed (Figures 3-4) there 

is an increased possibility of pouring water over your hand and into 

the bottle when rinsing (Figure 5). Once the cap is removed, turn your 

palm down to face the cap up (Figure 6), fill the inside of the cap with 

water (Figure 7), and empty it over the rim and threads of the bottle 

(Figure 8), being careful not to pour water over your finger and/or 

thumb or back into bottle (point mouth of bottle down, not up). Do 

about six cap and rim rinses then completely empty the bottle of any 

remaining DIW. Pour discard downstream or off-stream on land away 

from the sampling site. After the final rinse, place cap back on 1⁄4 turn, 

hold cap on with index finger of the hand holding the bottle. Now the 

sample rinses can be collected.

Figures 1 and 2. Correct way to remove cap for rinsing, palm facing away from 

bottle.

RIGHT! RIGHT!
4

Research Note RMRS-RN-49. 2012

Figures 3 and 4. Wrong way to remove cap for rinsing, palm facing the bottle.

Figure 5. Wrong way to hold cap for rinsing, palm up facing bottle.

WRONG WRONG

WRONG
5

Research Note RMRS-RN-49. 2012

Figure 6. Correct way to hold cap for rinsing, palm away from bottle.

Figure 7. Rinse cap with fingers and palm out of the way.

RIGHT!

RIGHT!
6

Research Note RMRS-RN-49. 2012

Figure 8. Rinse rim with water in cap, fingers and palm out of the way 

and bottle opening down.

Rinse Bottle with Sample Water

Return to your sampling point and reach as far into stream as possible. 

Hold the cap on the bottle with your index finger (Figure 9). Immerse 

the bottle completely 10 cm (4 inches) deep, or half way to bottom 

if the stream is shallow (write the depth the sample was collected on 

the field notes after the sample is collected and secured). If stream is 

too shallow to immerse the bottle fully, collect as much as possible, 

being very careful not to touch the bottom where sediments can 

be disturbed and make sure no surface film flows into the bottle. A 

syringe (appropriately rinsed three times) may be used to fill the bottle 

if necessary, but it is best to collect the sample directly into the bottle 

if possible. If a syringe is used, be sure to document this in the field 

notes.

Place the bottle flat on its side under water pointing the mouth of the 

immersed bottle upstream. Remove the index finger holding the cap 

from upstream once your other thumb and index finger of your other 

hand grips the cap. Remove the cap with the index finger and thumb 

RIGHT!
7

Research Note RMRS-RN-49. 2012

of your hand not holding the bottle, with your palm placed under or 

over the bottle to make sure it is not upstream (Figure 10). Be very 

careful that any water entering bottle does not touch your fingers/

gloves by making sure your hands and fingers are not upstream of 

the bottle when the cap is removed (Figure 11). Remove the cap 

enough to let water enter the bottle. Fill the bottle about half full. It 

is not necessary to fill the bottle for rinses. Place cap back on loosely 

(1⁄4 turn) under water, holding cap on with index finger of the hand 

holding the bottle. Always remove and replace the cap under water.

Rinse Bottle Three Times, Then Collect the Sample

Remove the immersed and capped bottle from the stream and shake. It 

is okay if some water leaks out rinsing the rim during shaking. Rinse 

procedure is the same as described for DIW. Rinse the cap and rim 

Figure 9. Hold cap 

on with your 

index finger 

to place bottle 

under water 

between rinses.

RIGHT!
8

Research Note RMRS-RN-49. 2012

Figure 10. Correct way to remove cap under water with palm under the bottle, 

hand not upstream.

Figure 11. Wrong way to remove cap under water with hand upstream.

RIGHT!

WRONG
9

Research Note RMRS-RN-49. 2012

about six times, being careful that rinse water does not touch your 

gloves. Rinsing must be conducted downstream of the sample site. The 

bottle opening needs to be pointed down during rinses to avoid rinse 

water flowing back into the bottle. This is easier if the bottle is only 

filled (or dumped) to half full for rim/cap rinses. After the six separate 

cap/rim rinses, pour out any remaining rinse water downstream of the 

sample point. Do not touch bottle mouth or inside of cap.

Collect stream water three separate times to do three complete bottle/

cap/rim rinses. If you lose count, collect and rinse again. Collect the 

final sample on the fourth immersion. Use the same procedure as before 

but fill the bottle completely. Tip the bottle mouth up to remove all air 

bubbles before capping. If necessary, squeeze the bottle slightly as the 

cap is tightened so no air remains in bottle. Be especially careful not to 

contaminate the sample with surface film or bottom sediment. If this 

happens, discard the sample and start your three rinses over. Place cap 

on and tighten under water. Remove from water and make sure that the 

cap is tight. If the stream is too shallow to immerse bottle fully when 

tipped up for filling, collect as much as possible, being very careful not 

to touch the surface or bottom. Note depth on field notes.

Stream Position to Take Water Sample

Depending on whether you are on the right side or left side of the 

stream facing upstream, and whether you are holding the bottle in 

your right hand or left hand, always be careful that your hand holding 

the bottle and your palm and fingers of the other hand tightening and 

loosening the cap is not upstream of the bottle opening.

Left side of stream, facing upstream: Hold the bottle with your right 

hand, cap pointing upstream. Remove cap with the index finger and 

thumb of your left hand with your palm placed under the bottle (palm 

and other fingers should not be upstream).

Right side of stream, facing upstream: Hold the bottle with your left 

hand, cap pointing upstream. Remove cap with the index finger and 

thumb of your right hand with your palm placed under the bottle (palm 

and other fingers should not be upstream).
10

Research Note RMRS-RN-49. 2012

Seal and Store Bottle for Transport

Once the final sample is collected, seal the sample bottle immediately 

in a zipper lock bag, place it in a cooler, and keep cold with frozen 

ice-packs or snow (place snow in double zipper lock bags). Do not 

place snow or ice in the same bag as the sample. Do not expose sample 

bottles to the sun.

Complete Miscellaneous Post-Sampling Tasks

After the sample is secured in the cooler, remove the gloves, rinse 

in stream, and place in a zipper lock bag. Before leaving the field 

site, make sure the field data sheet is completed. Note any unusual 

conditions such as wind or rain. Measure the air temperature 

(thermometer must be shaded) and record. When you return from the 

field, rinse the gloves (with DIW if available) and dry them out.

Shipping Instructions

Samples are filtered in the lab. Keep samples cool while transporting. 

Ship them overnight to the lab in a picnic cooler with frozen icepacks. 

The lab is not open weekends or holidays so do not ship the samples 

unless they can arrive at the lab Monday through Friday workdays. If 

you need to store the samples before shipping, keep them refrigerated at 

39-40oF (4o C) but do not freeze. Ship them using afternoon pickup for 

next day arrival. Hand delivery to the lab is preferred, or arrange for a 

contact to pick up the samples.

Duplicate and Blank Samples

Collect a duplicate sample if instructed. Generally, every 10th – 15th

sample collected is replicated (duplicated). Sample sites chosen for 

duplicate sampling are selected at random among streams or lakes 

sampled. If a duplicate is required for your site, repeat the same 

procedures as with the normal stream samples. The duplicate is the 

second of the two samples collected. Write “DUPL” on the sample 

bottle before the sample is collected. Duplicates document repeatability 

of individual sample collections and reproducibility of laboratory 

results.
11

Research Note RMRS-RN-49. 2012

Take a field blank sample bottle to the field if instructed. The field blank 

(FB) remains unopened. Write sample study area, stream or lake name, 

date and year, sampler’s name, and “FB” on the bottle. Field blanks are 

necessary to quantify chemicals from non-sample sources such as water 

bottles, DIW, filter paper, and handling procedures. The FB bottle is 

never opened in the field. However, the extra FB bottle can be used for 

the sample bottle in an emergency if the sample bottle or its cap is lost 

or contaminated. The FB is not as vital to collect as the sample.

Acknowledgments

Thanks to the numerous experienced field samplers that I have 

observed over the past 25 years who have helped me refine the final 

procedures. Thanks also to Andrea Holland-Sears for the photos taken 

during a training session August 2011, to Dave Richie for providing 

the demonstration for those photos, to Cass Cairns for the rim rinsing 

photo.

Information Sources for Surface Water Sampling

Information on the U.S. Forest Service Air Program Laboratory 

is available from a link at the U.S. Forest Service Air Resource 

Management website: www.fs.fed.us/air. Click on “Air Program 

Laboratory” at the Air Program website. Information on where to obtain 

water bottles, where to ship samples, and blank field forms is available 

here.

You may order additional copies of this publication by sending your mailing 

information in label form through one of the following media. Please specify the 

publication title and series number.

Publishing Services

Telephone (970) 498-1392

FAX (970) 498-1122

E-mail rschneider@fs.fed.us

Web site http://www.fs.fed.us/rm/publications

Mailing address Publications Distribution

Rocky Mountain Research Station

240 West Prospect Road

Fort Collins, CO 80526
The Rocky Mountain Research Station develops scientific information 

and technology to improve management, protection, and use of the 

forests and rangelands. Research is designed to meet the needs of 

the National Forest managers, Federal and State agencies, public and 

private organizations, academic institutions, industry, and individuals. 

Studies accelerate solutions to problems involving ecosystems, range, 

forests, water, recreation, fire, resource inventory, land reclamation, 

community sustainability, forest engineering technology, multiple use 

economics, wildlife and fish habitat, and forest insects and diseases. 

Studies are conducted cooperatively, and applications may be found 

worldwide.

Station Headquarters

Rocky Mountain Research Station

240 W Prospect Road

Fort Collins, CO 80526

(970) 498-1100

Research Locations

Reno, Nevada

Albuquerque, New Mexico

Rapid City, South Dakota

Logan, Utah

Ogden, Utah

Provo, Utah

The U.S. Department of Agriculture (USDA) prohibits discrimination in all of its 

programs and activities on the basis of race, color, national origin, age, disability, 

and where applicable, sex (including gender identity and expression), marital 

status, familial status, parental status, religion, sexual orientation, political 

beliefs, genetic information, reprisal, or because all or part of an individual’s 

income is derived from any public assistance program. (Not all prohibited bases 

apply to all programs.) Persons with disabilities who require alternative means 

for communication of program information (Braille, large print, audiotape, etc.) 

should contact USDA’s TARGET Center at (202) 720-2600 (voice and TDD).

To file a complaint of discrimination, write to: USDA, Assistant Secretary for Civil 

Rights, Office of the Assistant Secretary for Civil Rights, 1400 Independence 

Avenue, S.W., Stop 9410, Washington, DC 20250-9410. Or call toll-free at 

(866) 632-9992 (English) or (800) 877-8339 (TDD) or (866) 377-8642 (English 

Federal-relay) or (800) 845-6136 (Spanish Federal-relay). USDA is an equal 

opportunity provider and employer.

www.fs.fed.us/rmrs

Flagstaff, Arizona

Fort Collins, Colorado

Boise, Idaho

Moscow, Idaho

Bozeman, Montana

Missoula, Montana