National Water-Quality Assessment Program

Automated Routines for Calculating Whole-Stream

Metabolism: Theoretical Background and User’s Guide

Techniques and Methods 4–C2

Chapter 2 of

Book 4, Hydrologic Analysis and Interpretation,

Section C, Surface Water

Automated Routines for Calculating 

Whole-Stream Metabolism: Theoretical 

Background and User’s Guide

By Jerad D. Bales and Mark R. Nardi

Chapter 2 of 

Book 4, Hydrologic Analysis and Interpretation,

Section C, Surface Water

National Water-Quality Assessment Program

Techniques and Methods 4–C2

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2007

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Suggested citation:

Bales, J.D., and Nardi, M.R., 2007, Automated routines for calculating whole-stream metabolism—Theoretical background and user’s guide: U.S. Geological Survey Techniques and Methods 4–C2, 33 p. (online at http://pubs.water.

usgs.gov/tm4c2/)
iii

Foreword

The U.S. Geological Survey (USGS) is committed to providing the Nation with credible scientific information that helps to enhance and protect the overall quality of life and that 

facilitates effective management of water, biological, energy, and mineral resources (http://

www.usgs.gov/). Information on the Nation’s water resources is critical to ensuring long-term 

availability of water that is safe for drinking and recreation and is suitable for industry, irrigation, and fish and wildlife. Population growth and increasing demands for water make the availability of that water, now measured in terms of quantity and quality, even more essential to the 

long-term sustainability of our communities and ecosystems.

The USGS implemented the National Water-Quality Assessment (NAWQA) Program in 

1991 to support national, regional, State, and local information needs and decisions related to 

water-quality management and policy (http://water.usgs.gov/nawqa). The NAWQA Program is 

designed to answer: What is the condition of our Nation’s streams and ground water? How are 

conditions changing over time? How do natural features and human activities affect the quality 

of streams and ground water, and where are those effects most pronounced? By combining 

information on water chemistry, physical characteristics, stream habitat, and aquatic life, the 

NAWQA Program aims to provide science-based insights for current and emerging water issues 

and priorities. From 1991–2001, the NAWQA Program completed interdisciplinary assessments 

and established a baseline understanding of water-quality conditions in 51 of the Nation’s river 

basins and aquifers, referred to as Study Units (http://water.usgs.gov/nawqa/studyu.html). 

Multiple national and regional assessments are ongoing in the second decade (2001–2012) 

of the NAWQA Program as 42 of the 51 Study Units are reassessed. These assessments extend 

the findings in the Study Units by determining status and trends at sites that have been consistently monitored for more than a decade, and filling critical gaps in characterizing the quality of 

surface water and ground water. For example, increased emphasis has been placed on assessing the quality of source water and finished water associated with many of the Nation’s largest 

community water systems. During the second decade, NAWQA is addressing five national 

priority topics that build an understanding of how natural features and human activities affect 

water quality, and establish links between sources of contaminants, the transport of those contaminants through the hydrologic system, and the potential effects of contaminants on humans 

and aquatic ecosystems. Included are topics on the fate of agricultural chemicals, effects of 

urbanization on stream ecosystems, bioaccumulation of mercury in stream ecosystems, effects 

of nutrient enrichment on aquatic ecosystems, and transport of contaminants to public-supply 

wells. These topical studies are conducted in those Study Units most affected by these issues; 

they comprise a set of multi-Study-Unit designs for systematic national assessment. In addition, 

national syntheses of information on pesticides, volatile organic compounds (VOCs), nutrients, 

selected trace elements, and aquatic ecology are continuing. 

The USGS aims to disseminate credible, timely, and relevant science information to 

address practical and effective water-resource management and strategies that protect and 

restore water quality. We hope this NAWQA publication will provide you with insights and 

information to meet your needs, and will foster increased citizen awareness and involvement in 

the protection and restoration of our Nation’s waters. 
iv

The USGS recognizes that a national assessment by a single program cannot address all 

water-resource issues of interest. External coordination at all levels is critical for cost-effective 

management, regulation, and conservation of our Nation’s water resources. The NAWQA 

Program, therefore, depends on advice and information from other agencies—Federal, State, 

regional, interstate, Tribal, and local—as well as nongovernmental organizations, industry, academia, and other stakeholder groups. Your assistance and suggestions are greatly appreciated.

 Robert M. Hirsch

Associate Director for Water
v

Contents

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

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

Purpose and Scope ..............................................................................................................................2

Theoretical Background...............................................................................................................................2

Overview.................................................................................................................................................2

Dissolved-Oxygen Saturation Concentration...................................................................................4

Correction of Measured Dissolved-Oxygen Concentration for Sensor Error 

and Drift.....................................................................................................................................5

Determination of Analysis Period ......................................................................................................6

Reach-Averaged Water Temperature, Dissolved-Oxygen Concentration, 

and Dissolved-Oxygen Deficit...............................................................................................7

Reaeration..............................................................................................................................................8

Net Metabolism.....................................................................................................................................8

Respiration.............................................................................................................................................8

Gross Primary Production and Net Ecosystem Production.........................................................11

User’s Guide..................................................................................................................................................11

Two-Station Method...........................................................................................................................11

Site Data......................................................................................................................................11

Stream Metrics ..........................................................................................................................13

Meter—Importing Data ............................................................................................................15

Meter —Calculation of Dissolved-Oxygen Adjustments ....................................................20

Graph Meter Data—Automated Selection of Analysis Period ..........................................21

Meter and Graph Meter Data—Manual Selection of Analysis Period ............................22

Calculate Metabolism ..............................................................................................................25

Summary Output ........................................................................................................................27

Data Archive...............................................................................................................................28

Single-Station Method.......................................................................................................................28

References....................................................................................................................................................32

Figures

1. Flow chart showing steps in metabolism calculations ..........................................................3

2. Schematic diagram showing initial error and sensor drift....................................................5

3. Typical photosynthetically active radiation and dissolved-oxygen concentration 

data collected at Athanum Creek at Union Gap, Washington, August 18–20, 2003 ..........6

4. Example rhodamine dye curves used for estimating reach travel time, 

Skull Creek near Linwood, Nebraska, July 15, 2003................................................................7

5. (A) Measured upstream and downstream dissolved-oxygen concentrations for 

150-meter reaches at Skull Creek near Linwood, Nebraska, and Clear Creek near 

Columbus, Nebraska, and (B) calculated gross primary production and respiration for 

Skull Creek and Clear Creek for a range of reaeration rate coefficients............................9

6. Calculated daytime respiration for Athanum Creek at Union Gap, Washington, 

August 19, 2003............................................................................................................................11
vi

7–9. Screen captures of the:

7. Site Data page in the Stream Metabolism Program...................................................13

8. Stream Metrics page in the Stream Metabolism Program .......................................14

9. Unpopulated Meter page in the Stream Metabolism Program.................................15

10. Example of text file format required for importing water-quality data 

into the Stream Metabolism Program.....................................................................................16

11–14. Screen captures of:

11. The Meter page populated with data from upstream and downstream 

water-quality meters, and prior to importing light-meter data, in the 

Stream Metabolism Program..........................................................................................16

12. A section of Meter page in the Stream Metabolism Program showing a 

boundary that can be dragged to expand column width and full column 

headings for upstream water temperature and upstream specific 

conductance data.............................................................................................................17

13. A Meter page in the Stream Metabolism Program showing condition in 

which data were collected at only one of the two in situ water-quality 

meters for a portion of the deployment period ............................................................18

14. The Meter page in the Stream Metabolism Program showing 

rows selected for copying into a spreadsheet application .......................................18

15. Example of file format required for importing light-meter data into the Stream 

Metabolism Program..................................................................................................................19

16–18. Screen captures of the:

16. Meter page in the Stream Metabolism Program populated with 

water-quality monitoring data and light-meter data...................................................19

17. Meter Drift section of the Meter page used for dissolved-oxygen 

sensor drift calibration in the Stream Metabolism Program.....................................20

18. Instrument Drift window for entering beginning and ending errors 

in dissolved-oxygen meter readings in the Stream Metabolism Program..............21

19. Automatically graphed data showing time-series plots of dissolved-oxygen 

concentration, water temperature, and photosynthetically active radiation, 

though not to scale, and identified gross primary production calculation periods, 

as a feature of the Stream Metabolism Program..................................................................21

20. Screen capture of the Meter page showing user-selected daylight beginning 

time in the Stream Metabolism Program................................................................................23

21. Automatically re-graphed data after manually selecting a daylight period in the 

Stream Metabolism Program....................................................................................................23

22–34. Screen captures of:

22. The Graph Meter Data page showing manually entered nighttime periods 

in the Stream Metabolism Program...............................................................................24

23. The Graph Meter Data page following manual entry of all analysis 

period information in the Stream Metabolism Program.............................................24

24. The Graph Meter Data page showing graphical selection of the 

beginning of the daylight period for graphical analysis in the Stream 

Metabolism Program........................................................................................................25

25. The Calculate Metabolism page in the Stream Metabolism Program....................26

26. The Calculate Metabolism page showing reach-averaged calculations 

in the Stream Metabolism Program...............................................................................26

27. The Summary Output page in the Stream Metabolism Program.............................27

28. The populated Data Archive page in the Stream Metabolism Program.................28
vii

29. An unpopulated Data Archive page in the Stream Metabolism Program .............29

30. The Site Data page for single-station application in the Stream 

Metabolism Program........................................................................................................29

31. The Stream Metrics page for single-station application in the Stream 

Metabolism Program........................................................................................................30

32. The Meter page for single-station application in the Stream Metabolism 

Program..............................................................................................................................30

33. The Calculate Metabolism page for single-station application in the 

Stream Metabolism Program..........................................................................................31

34. The Summary Output page for single-station application in the Stream 

Metabolism Program........................................................................................................32

Table

1. Required and optional data for the Stream Metabolism Program .....................................12

Conversion Factors

SI to Inch/Pound

Multiply By To obtain

Length

centimeter (cm) 0.3937 inch (in.)

millimeter (mm) 0.03937 inch (in.)

meter (m) 3.281 foot (ft) 

meter (m) 1.094 yard (yd) 

Area

square meter (m2) 10.76 square foot (ft2) 

Volume

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

liter (L) 2.113 pint (pt)

liter (L) 1.057 quart (qt)

liter (L) 0.2642 gallon (gal)

liter (L) 61.02 cubic inch (in3

) 

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)

kilogram (kg) 2.205 pound avoirdupois (lb)

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).

Elevation, as used in this report, refers to distance above the vertical datum.

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius (μS/cm at 25 °C) or in 

millisiemens per centimeter at 25 degrees Celsius (mS/cm at 25 °C).

Concentrations of chemical constituents in water are given either in milligrams per liter (mg/L) or 

micrograms per liter (μg/L).
viii

Abbreviations

C concentration 

Cf units conversion factor

Cs saturation concentration

d day

Davg reach-averaged dissolved-oxygen deficit

DO dissolved oxygen, in milligrams per liter 

DOcorrected dissolved-oxygen concentration corrected for initial error, fouling, and drift

DOd dissolved-oxygen concentration at downstream measuring station

DOP dissolved-oxygen solubility at barometric pressure (Patm)

DOreading uncorrected DO concentration obtained directly from the water-quality meter

DOs dissolved-oxygen saturation concentration

DOsl dissolved-oxygen solubility, in milliliters per liter

DOu dissolved-oxygen concentration at upstream measuring station

dt measurement interval

Ee error in dissolved-oxygen reading at the end of meter deployment

Ei error in dissolved-oxygen reading at the beginning of meter deployment

Fr reaeration flux

GPP gross primary production

hr hour

K2 reaeration rate coefficient

min minute

mm Hg millimeters of mercury

μmol/(m2/s) micromoles per square meter per second

Ni serial number of current water-quality meter reading, with the first reading 

having a serial value of 0

Ntotal total number of readings during water-quality meter deployment 

n1 number of individual metabolism flux values during the first nighttime period

n2 number of individual metabolism flux values during the second nighttime 

period

nd the total number of measurement intervals during daylight hours, including the 

first and last daylight readings

NM net metabolism flux

NAWQA National Water-Quality Assessment Program 

NEET Nutrient Enrichment Effects Team

NEP net ecosystem production 

NPP net primary production

P photosynthesis

Patm ambient barometric pressure

Psat saturation vapor pressure

PAR photosynthetically active radiation 

Q streamflow

R respiration

Rc community respiration

Rd daytime respiration

Rcon constant daytime respiration

Rp plant respiration

Rpre-dawn the average respiration rate calculated from individual net metabolism fluxes 

for the 1-hour period immediately before dawn

Rpost-sunset the average respiration rate calculated from individual net metabolism fluxes 

for the 1-hour period immediately after sunset

Rvar(t) variable daytime respiration at time (t)
ix

S salinity SN1 sum of net metabolism flux for the first nighttime period SN2 sum of net metabolism flux for the second nighttime period

SC specific conductance, in millisiemens or microsiemens per centimeter

sec seconds

SMP Stream Metabolism Program t time

T water temperature, in degrees Celsius Td duration of the daytime period, in hours TK water temperature, in degrees Kelvin TN1 duration of the first nighttime period, in hours TN2 duration of the second nighttime period, in hours Tt travel time through reach tu time at which upstream measurement is made U mean stream velocity

USGS U.S. Geological Survey VD measured downstream value VR reach-averaged value VU measured upstream value

x longitudinal distance along a stream

Abstract 

In order to standardize methods and facilitate rapid 

calculation and archival of stream-metabolism variables, the 

Stream Metabolism Program was developed to calculate gross 

primary production, net ecosystem production, respiration, 

and selected other variables from continuous measurements of 

dissolved-oxygen concentration, water temperature, and other 

user-supplied information. Methods for calculating metabolism from continuous measurements of dissolved-oxygen 

concentration and water temperature are fairly well known, 

but a standard set of procedures and computation software for 

all aspects of the calculations were not available previously. 

The Stream Metabolism Program addresses this deficiency 

with a stand-alone executable computer program written in 

Visual Basic.NET®, which runs in the Microsoft Windows®

environment. 

All equations and assumptions used in the development 

of the software are documented in this report. Detailed 

guidance on application of the software is presented, along 

with a summary of the data required to use the software. Data 

from either a single station or paired (upstream, downstream) 

stations can be used with the software to calculate metabolism 

variables.

Introduction

Stream metabolism is the net gain in dissolved 

oxygen (DO) associated with photosynthesis and the loss 

of DO through plant and animal respiration. Odum (1956) 

developed, and gave to it the now commonly used name, the 

upstream-downstream method of measuring community, or 

whole-stream metabolism, within a stream reach. Application 

of the method involved 1- to 6-hour (hr) measurements of DO 

concentration and water temperature (T), estimation of reaeration rate, and graphical data analysis of DO concentration (for 

example, Erdmann, 1979). 

Whole-stream metabolism measurements have improved 

with the introduction of instrumentation that automatically 

measures and records DO, T, and other parameters (for 

example, Wagner and others, 2006) at short time intervals. 

The development of tracer-gas methods (Tsivoglou and others, 

1968; Rathbun and others, 1978; Kilpatrick and others, 1989) 

to measure stream reaeration rates directly can reduce uncertainty in metabolism computations. Other improvements in the 

whole-stream metabolism method (Marzolf and others, 1994), 

including the continuous measurement of photosynthetically 

active radiation (PAR), have resulted in increased use of the 

procedure to understand stream ecosystem functioning.

Despite some standardization in measurement and data 

analysis procedures, metabolism variables can be calculated 

from the same set of whole-stream data using slightly different 

approaches. For example, daylight respiration (R) typically is 

extrapolated from nighttime R, but the exact value of nighttime 

R that is used and the method of extrapolation are subject to 

judgment. No protocol or standard software tool currently 

is available for computing whole-stream metabolism from 

continuous measurements of DO and T.

In 2001, the U.S. Geological Survey (USGS) National 

Water-Quality Assessment (NAWQA) Program began an 

intensive study of nutrient enrichment—elevated concentrations of nitrogen and phosphorus—in streams draining 

agricultural basins across the Nation (Munn and Hamilton, 

2003). One of the major objectives of this study is to 

determine the interrelations among nutrient conditions, algal 

communities, and stream metabolism.

As a part of the nutrient-enrichment study, which is 

conducted by the NAWQA Nutrient Enrichment Effects Team 

(NEET) and other NAWQA studies, whole-stream metabolism 

measurements have been, or are planned to be, made at more 

than 100 individual sites, with some replication of measurements at a subset of the sites. As previously noted, methods 

for calculating metabolism from continuous measurements of 

DO and T are fairly well known, although no standard set of 

procedures is available for all aspects of the measurements and 

calculations. In order to standardize methods and to facilitate 

rapid calculation and archival of stream-metabolism variables 

National Water-Quality Assessment Program

Automated Routines for Calculating Whole-Stream 

Metabolism: Theoretical Background and User’s Guide

By Jerad D. Bales and Mark R. Nardi
2 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

for the large number of NAWQA study sites, the Stream 

Metabolism Program (SMP) was developed. 

Purpose and Scope

The purpose of this report is to document the Stream 

Metabolism Program (SMP). The SMP is a stand-alone 

executable computer program written in Visual Basic.NET®, 

which runs in the Microsoft Windows® environment. The 

program calculates gross primary production, net ecosystem 

production, respiration, and selected other variables from 

continuous measurements of DO, T, and other user-supplied 

information. Data from either a single station or paired 

(upstream, downstream) stations can be used in the SMP to 

calculate metabolism variables.

The equations and assumptions used in the development 

of the software are documented in this report. Detailed guidance on application of the software is then presented, along 

with a summary of the data required to use the software. 

Theoretical Background

The SMP was developed to facilitate computation of 

selected measures of stream metabolism using procedures 

first described by Odum (1956). This method is also known as 

the diurnal curve method because the method was first based 

on a graphical analysis of a plot of one or more days of DO 

in relation to time (for example, Erdmann, 1979). Data from 

either a single station or from two stations, one each at the 

upstream and downstream ends of the reach, can be used in the 

analysis. The theory supporting calculations by the SMP and 

all assumptions made in the application of the software are 

described in this section.

Overview

Detailed discussions of the processing of oxygen in 

streams can be found in a number of works, including Hauer 

and Lamberti (2006). Primary productivity is “the rate of 

formation of organic matter from inorganic carbon by photosynthesizing organisms and thus represents the conversion of 

solar energy to reduced chemical energy” (Bott, 2006). Some 

of the production is lost through plant respiration, Rp, so 

 GPP = NPP + Rp, 

 

where 

GPP = gross primary production, and

NPP = net primary production, which is the portion 

of GPP stored in plant biomass. 

The variables in eq. 1 typically are expressed in units of mass 

of oxygen per unit wetted stream area per time (for example, 

grams of oxygen per square meter per day). Equation 1 applies 

strictly to production and respiration by plants in the stream.

The change in DO concentration is an indication of the 

DO additions by reaeration and photosynthesis and DO losses 

by community respiration, Rc, which is respiration by both 

plants (Rp), or autotrophs, and heterotrophs, such as bacteria 

and insects. Estimates of R typically are based on measurements at night (or in the dark) when production is zero. 

Respiration during daylight often is assumed to be equal to 

nighttime R, so if daylight R differs substantially from nighttime R, estimates of plant GPP could be in error. Moreover, if 

heterotrophic respiration is a large part of Rc, the Rc measurements will not provide a good estimate of Rp

, resulting in 

additional error in estimates of GPP. Heterotrophic respiration 

is often a large part of Rc when the stream receives high loads 

of carbonaceous, nitrogenous, or chemical oxygen demand 

from human-related sources or when streams are shaded and 

lack sufficient sunlight to maximize plant production. Because 

community respiration, and not plant respiration, is measured 

in the whole-stream metabolism method, eq. 1 may be more 

appropriately written as

 GPP = NEP + Rc, 

 

where NEP = net ecosystem production.

The mass balance for a gas in a stream, which is the 

basis for the whole-stream metabolism calculation method 

(Ramaswami and others, 2005), is

where

C = concentration, in (mass/volume);

Cs = saturation concentration, in (mass/volume);

t = time;

U = mean stream velocity, in (length/time); 

x = longitudinal distance along the stream 

channel; and 

K2 = air-water gas exchange (or reaeration) 

coefficient, in (1/time).

Equation 3 is based on the assumption that stream velocity is 

constant (steady flow) over the period of measurements and 

that there is no dispersion in the study reach. 

Equation 3 can be simplified for selected conditions. If 

no ground-water or surface-water inputs are within the stream 

reach under consideration, the sources of DO to the reach are 

inflow at the upstream end, photosynthesis (P), and reaeration. 

The losses of DO are a result of outflow at the downstream 

end of the reach, deoxygenation in the case of super-saturated 

water, and Rc. Reaeration, P, and Rc can vary with time, even 

under steady flow conditions, primarily because of the effects 

of changes in water temperature and light. 

(1)

(2)

(3) 2

()() () , s s

s

CC CC U K C C sources losses

t x

∂− ∂−

= + −+ −

∂ ∂
Theoretical Background 3

The single-station method for estimating stream metabolism is valid only if the first term on the right side of eq. 3 

is zero, or in other words, if the longitudinal gradient of the 

DO deficit (dissolved-oxygen saturation minus DO) is zero. 

The two-station method provides a measure of metabolism 

in a parcel of water flowing through the study reach. These 

values can be summed over a day to provide estimates of daily 

metabolism.

The SMP requires some site-specific data and time-series 

data. Data typically are obtained by using continuously 

recording water-quality meters that are deployed for at least 

36 hours. The program produces graphs of the time-series 

data, corrects DO readings for sensor error and drift during 

deployment, summarizes data, calculates metabolism variables, and provides the user with options for exporting data to 

a spreadsheet or text files (fig. 1). Calculations performed by 

the SMP are

•	 Percent of saturation concentration for each DO 

reading;

•	 Adjustment of each DO reading for meter error, 

fouling, and drift;

•	 Automated selection of metabolism analysis periods;

•	 Reach-averaged values for water temperature, DO, and 

DO saturation concentration (DOs);

•	 Reaeration flux for each time step;

•	 Net metabolism flux at each time step; 

•	 Community respiration at each time step and 24-hour 

respiration; and

•	 Gross primary production and net ecosystem 

production.

Details of each of these calculations within the SMP are 

described in the following sections.

Single-station or

two-station data?

Figure 1. Flow chart showing steps in metabolism calculations. (Yellow boxes indicate decisions to be made by user.)
4 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

Dissolved-Oxygen Saturation Concentration

The first calculation in the SMP is the determination of 

the DO saturation concentration (DOs). The saturation concentration is the DO concentration in the stream at 100 percent 

saturation for a given water temperature, barometric pressure, 

and specific conductance.

The accepted relation for saturation concentration at 

the vertical datum (North American Vertical Datum of 1988 

[NAVD 88]; Weiss, 1970) is

ln(DOsl) = [A1 + A2*(100/TK) + A3*ln(TK/100)

 +A4*(TK/100)] + S*[B1 + B2*(TK/100)

 +B3*(TK/100)2]

where

Al = –173.4292; 

A2 = 249.6339; 

A3 = 143.3483;

A4 = –21.8492; 

Bl = –0.033096;

B2 = 0.014259;

B3 = –0.001700;

TK = temperature, in degrees Kelvin, = (273.15 

+ T);

S = salinity, in grams per kilogram or parts per 

thousand; 

DOsl = dissolved oxygen solubility, in milliliters 

per liter at NAVD 88; 

ln = natural logarithm; and

barometric pressure at NAVD 88 = 760 millimeters of 

mercury.

DOsl, in milliliters per liter, can be converted to the more 

standard units of milligrams per liter by multiplying DOsl in 

milliliters per liter by 1.4276 (U.S. Geological Survey, 1981).

A simple conversion from specific conductance to salinity 

(U.S. Geological Survey, 1981) is 

S = 5.572*10–4*SC + 2.02*10–9*SC*SC, 

where SC = specific conductance, in microsiemens per centimeter at 25 degrees Celsius. Equation 5 is not particularly 

accurate for converting specific conductance to salinity, but the 

error in conversion given by eq. 5 has negligible effect on the 

calculation of DO solubility from eq. 4, and eq. 5 is much simpler to program than the more accurate relations (for example, 

Lewis, 1980). 

The correction of eq. 4 for barometric pressure (U.S. 

Geological Survey, 1981) is

DOp = DOsl * (( Patm – Psat) / (760 – Psat)) , 

where

DOp = saturation concentration, in milligrams 

per liter, at barometric pressure Patm, in 

millimeters of mercury;

DOsl = saturation concentration, in milliliters per 

liter at NAVD 88, calculated from eq. 4; 

Patm = ambient barometric (or atmospheric) 

pressure; and

Psat = saturation vapor pressure, in millimeters of 

mercury, as described below.

Several formulations are available for calculating saturation vapor pressure of water (Vomel, 2004). At temperatures 

greater than about 0 degrees Celsius (oC), the various formulations give essentially the same result. The Bolton (1980) 

equation is one of the simpler equations (with temperature in 

degrees Celsius): 

Psat = 4.5844 * exp[17.67*T/(T + 243.5)]. 

The general relation for DO saturation concentration 

(DOs, in milligrams per liter) in natural waters at any barometric pressure, water temperature (greater than 0 o

C), and 

specific conductance is obtained by combining eqs. 4–7: 

DOs = (1.4276*exp(–173.4292 +(249.6339

 *((100/(T+273.15))))+(143.3483

 *(ln((T+273.15)/100))) –(21.8492*((T+273.15)/100))

 +(((0.0005572*SC)+(0.00000000202*SC*SC))

 *(–0.033096+(0.014259*((T+273.15)/100))

 –(0.0017*((T+273.15)/100)*((T+273.15)/100))))))

 *((Patm–(7.50062*0.6112*exp(17.67

 *(T/(T+243.5)))))/(760–(7.50062*0.6112*exp

 (17.67*(T/(T+243.5)))))). 

Although barometric pressure changes during a wholestream metabolism measurement period during which meters 

are deployed, a single value of barometric pressure is used in 

the SMP for all DOs calculations for each meter deployment 

because changes in Patm that are likely to occur during a 

24- to 72-hr deployment do not substantially affect DOs. For 

example, at a temperature of 20 oC and a specific conductance 

of 150 microsiemens per centimeter (μS/cm), DOs is 9.00 milligrams per liter (mg/L) at Patm = 755 millimeters (mm) 

mercury (Hg) and 9.12 mg/L at Patm = 765 mm Hg. Moreover, 

continuous records of barometric pressure at the deployment 

site typically are not available. Saturation concentration is 

calculated in the SMP for each measurement interval by using 

T-, SC-, and DO-concentration data for the measurement 

intervals and the constant barometric pressure. Barometric 

pressure should be recorded when instruments are deployed 

and recovered, and an average pressure can be used in the 

calculations.

(4)

(5)

(6)

(7)

(8)
Theoretical Background 5

Correction of Measured Dissolved-Oxygen 

Concentration for Sensor Error and Drift 

Measured DO concentrations are corrected for initial 

calibration error and for sensor fouling and calibration drift 

that can occur during the deployment (fig. 2). The initial 

calibration error (corrected DO minus measured DO) is added 

to all DO readings. The total ending error (sensor fouling 

plus calibration drift) is determined, and this error is linearly 

interpolated over time and added to each field reading. This 

approach is consistent with published USGS methods (Wagner 

and others, 2006) and is described by the following equation:

DOcorrected = DOreading + (Ei + (((Ee–Ei)/Ntotal – 1 )*Ni)), 

 

where 

DOcorrected = DO concentration, in milligrams per liter, 

corrected for initial error, fouling, and 

drift;

DOreading = field-measured DO concentration, in 

milligrams per liter;

Ei = error in DO reading, in milligrams per liter, 

at the beginning of deployment;

Ee = error in DO reading, in milligrams per liter, 

at the end of deployment;

Ntotal = total number of readings during 

deployment; and

Ni = serial number of current meter reading, with 

the first reading having a serial value of 0.

The corrected DO value for the first reading (Ni = 0) is equal 

to the DO reading plus the initial error (Ei). Equation 9 is 

based on the assumption that field readings are made at equal 

time increments throughout the deployment. 

Drift is calculated by the SMP as follows. Following 

meter calibration, DO readings are made in saturated air prior 

to deployment (pre-deployment); these readings are repeated 

after the meter is recovered (post-deployment). About four 

to six individual readings should be made at relatively short 

increments (3–5 minutes). Barometric pressure should be 

noted for pre- and post-deployment readings. The DO reading 

in saturated air should be equal to the DOs concentration 

for the measured temperature and barometric pressure if the 

meter is exactly correct. Differences between the actual DO 

reading in saturated air and the Cs (obtained by using eq. 8) 

are calculated by the SMP for each reading during the pre- and 

post-deployment periods. The differences for each measurement interval are averaged for the pre-deployment period 

(Ei); a similar average is calculated for the post-deployment 

period (Ee). The error is positive if the DO reading is less than 

the saturation concentration, because the error is added to 

the reading to get the corrected value (eq. 9). This approach 

assumes that there are no errors in the temperature, specific 

conductance, and barometric pressure sensors, but that all of 

the error is associated with the DO sensor. This a reasonable 

assumption for a relatively short (1–5 days) deployment in 

waters that are not highly polluted.

 As previously noted, the SMP accepts a single value of 

barometric pressure for the entire deployment period. Large 

differences in barometric pressure between pre-deployment 

and post-deployment meter calibrations can result in small 

errors in Ei and Ee. For example, at typical stream temperatures 

(5–35 oC) and specific conductance values (2–20 millisiemens 

per centimeter [mS/cm]), a change in barometric pressure of 

10 mm Hg results in about a 1.3 percent change in DOs. The 

SMP allows users to directly input Ei and Ee when automated 

calculation of these values is not appropriate.

The approach used by the SMP to adjust DO readings 

for initial error, drift, and sensor fouling 

is based on the assumption that the 

correction can be linearly prorated by 

time over the deployment period. This 

is a reasonable assumption for the 

relatively short deployment periods 

typical of stream metabolism studies. 

Wagner and others (2006) suggest that 

the correction be linearly interpolated 

based on the final percentage error rather 

than the final measured error when the 

total error is large relative to the range in 

DO. This approach may be appropriate, 

for example, when the final DO error is 

2 mg/L, and the range in readings is, for 

example, 4 mg/L. In this case, Ei and Ee

should be computed by the user outside 

the SMP and then entered directly into 

the software, as demonstrated in the 

User’s Guide section of this report. 

A third method for correcting meter readings is provided by Wagner and others 

(9)

Figure 2. Schematic diagram showing initial error and sensor drift. Correct Dissolved Oxygen − Measured Dissolved Oxygen, in milligrams per liter

Drift, after correcting initial

reading to zero

Drift, based on initial

and final readings

Dissolved oxygen correction at time t

Initial error: correct

Initial reading to zero TIME
6 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

(2006) for use when the meter calibration is not linear over 

the range of readings. Modern in situ water-quality meters 

typically exhibit linear calibrations over the range of readings 

in flowing freshwater. 

Determination of Analysis Period

The SMP offers two options for identifying the daylight 

and nighttime periods for which metabolism variables are to 

be calculated—an automated selection of the analysis period 

by the SMP or user-specified analysis periods. A combination 

of the two options also is available, in which the analysis 

period is automatically selected, and the user can adjust 

selected features of the analysis period (see the User’s Guide

section of this report). A continuous record of PAR data are 

required for the automated approach. The analysis periods 

should include a complete sunrise to sunset daylight period 

and at least one nighttime period that immediately precedes 

and one that immediately follows the daylight analysis period. 

Methods used in the automated selection of the analysis period 

are described in this section. 

If the automated selection is used, the analysis period 

begins at the minimum DO concentration on the first night 

(fig. 3). The period then extends forward for at least 24 hr and 

includes the minimum DO concentration on the following 

night. If the minimum DO on the second night occurs more 

than 24 hr after the minimum on the first night, the calculation 

period is greater than 24 hr. Respiration values are prorated so 

that 24-hr respiration is reported. 

The analysis period is subdivided into daylight, night, 

pre-dawn, and post-sunset times (fig. 3). The daylight period 

is determined automatically by the SMP from the PAR data: 

the beginning of daylight is when the PAR reading exceeds 

2 micromoles per square meter per second [μmol/(m2/s)] and 

daylight ends when PAR becomes less than 2 μmol/(m2/s) 

(fig. 3). PAR values typically are constant through the nighttime, increase quickly from the nighttime levels at sunrise, and 

do not ever approach the threshold of 2 μmol/(m2/s) during 

daylight hours (fig. 3).

After the daylight period is determined from the PAR 

data, the SMP automatically assigns a 1-hr pre-dawn period 

that begins 1 hr before the beginning of the daylight period. 

Similarly, a 1-hr post-sunset period is automatically assigned, 

beginning immediately after the end of daylight (fig. 3). The 

pre-dawn and post-sunset periods are used for computing 

daytime respiration, as discussed in a subsequent section. 

Figure 3. Typical photosynthetically active radiation and dissolved-oxygen concentration data collected at Athanum Creek 

at Union Gap, Washington, August 18–20, 2003.

450

400

350

300

250

200

150

100

50

0

PHOTOSYNTHETICALLY ACTIVE RADIATION, IN MICROMOLES

PER SQUARE METER PER SECOND

12

10

8

6

4

2

0

DISSOLVED-OXYGEN CONCENTRATION, IN MILLIGRAMS PER LITER

Daylight ends

Daylight begins

Pre-dawn begins

Daylight ends

Daylight begins

Post-sunset ends

End of calculation period

Beginning of calculation period

Night Daylight Night

Photosynthetically active radiation

Dissolved-oxygen concentration

Beginning minimum

dissolved-oxygen concentration

1800 2100 0000 0300 0600

August 19, 2003 August 20, 2003

0900 1200 1500 1800 2100 0000 0300 0600 0900

Ending minimum

dissolved-oxygen concentration,

24 hours after beginning minimum
Theoretical Background 7

Two nighttime periods previously were noted. The 

first nighttime period begins at the time the minimum DO 

concentration occurs prior to the daylight period and extends 

to the beginning of the pre-dawn period (fig. 3). The second 

nighttime period begins at the end of the post-sunset period 

and extends to the time when the minimum DO concentration 

is recorded following the daylight period (fig. 3).

In some cases, the DO data may differ from the typical 

conditions shown in figure 3. In those cases, the user must 

select the beginning of the first nighttime period and the end 

of the second nighttime period (fig. 3). The SMP still will 

automatically identify the daylight, pre-dawn, and post-sunset 

periods. This approach is described in the User’s Guide

section of this report.

Reach-Averaged Water Temperature, 

Dissolved-Oxygen Concentration, and 

Dissolved-Oxygen Deficit

For the two-station method, reach-averaged values of 

water temperature, DO, and DO deficit [DOs(t) – DO(t)] are 

needed to solve eq. 3 for a parcel of water moving through the 

study reach. These values are calculated for each measurement time (t). The travel time (Tt

) of each water parcel is 

determined from measurements of time-of-travel made by 

using a conservative tracer, such as rhodamine dye or bromide 

(Kilpatrick and Wilson, 1989; fig. 4). The reach-averaged 

value is calculated as follows:

VR(t) = [VU(t–Tt) + VD(t)]/2, 

 

where

VR(t) = reach-averaged value at a given 

measurement time;

VU(t–Tt) = measured upstream value at a given 

measurement time minus the travel time 

(Tt); and 

VD(t) = measured downstream value at a given 

measurement time.

Equation 10 applies to T, DO, and DO deficit, but only 

strictly applies if the travel time is an integer multiple of the 

measurement interval (dt). For example, if the measurement 

interval is 5 minutes (min), the travel time must be 5 min, 

10 min, 15 min, and so on. Reach-averaged values are 

60

50

40

30

20

10

0

DYE CONCENTRATION, IN MICROGRAMS PER LITER

0 2,000 4,000 6,000 8,000 10,000 12,000

Travel time

Upstream

Downstream

CUMULATIVE TIME, IN SECONDS

Figure 4. Example rhodamine dye curves used for estimating reach travel time, Skull Creek near Linwood, Nebraska, 

July 15, 2003.

(10)
8 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

estimated when the travel time is not an integer multiple of the 

measurement interval as in the following:

 VR(t) = [VU(t

u

) + VD(t)]/2, 

 

where VU(t

u

) = upstream value at the measurement time (t

u

), 

for which t

u

 – (t –Tt) is minimized. For example, if t = 11:15, 

Tt = 8.0 min, and the water-quality measurement interval = 

5.0 min, the reach-averaged values would be calculated from 

downstream measurements at t = 11:15 and upstream measurements at t

u

 = 11:05. If Tt = 7.0, the reach-averaged values 

would be calculated from downstream measurements at t = 

11:15 and upstream measurements at t

u

 = 11:10.

Reaeration

Dissolved-oxygen flux across the air-water interface is 

calculated as follows:

 Fr(t) = Davg * K2(T) * Q * Tt* Cf , 

 

where 

Fr(t) = reaeration flux at time = t, in mass per time;

Davg = reach-averaged DO deficit calculated by 

using eq. 10 or 11, in mass per volume;

K2(T) = reaeration rate coefficient at water 

temperature (T), in 1/(t);

Q = streamflow, in volume per time;

Tt = travel time; and

Cf = units conversion factor.

Note that Fr is positive when the DO deficit is positive (DO 

concentration is less than the saturation concentration); a positive Frmeans that oxygen is being transferred from the atmosphere into the stream. Fr

 is calculated for each measurement 

interval and typically is reported in milligrams per minute 

when K2 is given in 1/min. 

The reaeration rate coefficient at any temperature (T) can 

be calculated from K2(T=20) by using the equation of Elmore 

and West (1961), which is the following:

 K2(T) = K2(T=20) * 1.024(T – 20). 

 

This equation can be rewritten as

K2(T) = K2(T=20) * (1+((T–20) * 0.0241)). 

 

Empirical relations for estimating K2 from stream 

characteristics typically give K2 at 20 oC. If K2 is measured in 

the field using tracer-gas or other methods, eq. 13 is used first 

to adjust the field-measured K2 to 20 oC. Then, K2 is calculated 

for each measurement interval by using eq. 14 with the 

reach-averaged temperature for the measurement interval. As 

an example, assume the temperature when K2 was measured 

in the field to be 0.092/min at a water temperature of 14.6 oC. 

Further, assume the water temperature at a given measurement 

interval is 23 oC. Then, successive applications of eq. 13 gives 

the field-measured K2 adjusted to 20 oC as 0.1046/min, and the 

K2(T=23) is 0.1123/min. 

The K2 can have a substantial effect on metabolism 

calculations, as demonstrated in figure 5. In this figure, T, DO, 

and site data from Skull Creek near Linwood, Nebraska, and 

Clear Creek near Columbus, Nebraska, were used to calculate 

Rc and GPP. K2 values were calculated for each site using 

29 individual empirical reaeration-rate estimation equations, 

and the lines in figure 5B extend over the range of those 

estimated K2 values. At Skull Creek (fig. 5A), there is little 

difference between upstream and downstream DO curves; as a 

result, estimates of GPP and R are relatively insensitive to K2

(fig. 5B). In contrast, the upstream and downstream maximum 

DO at Clear Creek differ by about 2 mg/L (fig. 5B), and GPP

and R are quite sensitive to changes in K2, with R varying by 

a factor of 5, depending on the empirical equation used to 

estimate K2. It also is noteworthy that the best estimate of K2

for Clear Creek is very near the condition at which the stream 

transitions from net DO production (GPP is greater than R) to 

net DO consumption (autotrophic to heterotrophic). Using the 

best estimate of K2, Clear Creek is determined to be autotrophic, but if a K2

 value that is 10 percent less than the best 

estimate of K2 is used to calculate GPP and R, the conclusion 

is that the stream is heterotrophic under the measured 

conditions.

Net Metabolism 

Net metabolism is the net change in DO in the study 

reach during a time interval, and represents the combined 

effects of photosynthesis and respiration on DO, minus any 

effects from reaeration. During the nighttime, net metabolism 

is assumed to be equal to respiration. Net metabolism is 

calculated at each measurement time as

NM(t) = {[DOd(t) – DOu(t–Tt)] * Q} – Fr(t), 

 

where

NM(t) = net metabolism flux at time (t), in mass/

time;

DOd(t) = downstream DO concentration at time (t); 

and

DOu(t – Tt) = upstream DO concentration at time (t) – Tt.

Respiration

Community respiration includes metabolism by 

heterotrophs (microbes and insects) and autotrophs (plants 

and selected bacteria) and can be directly measured only in 

darkness. Daytime respiration often is determined by some 

type of extrapolation of nighttime respiration. This approach, 

however, can be subject to errors associated with temperaturedependent respiration, light-dependent photorespiration by 

(11)

(12)

(13)

(14)

(15)
Theoretical Background 9

Figure 5. (A) Measured upstream and downstream dissolved-oxygen concentrations for 150-meter reaches 

at Skull Creek near Linwood, Nebraska, and Clear Creek near Columbus, Nebraska, and (B) calculated gross 

primary production and respiration for Skull Creek and Clear Creek for a range of reaeration rate coefficients.

14

12

10

8

6

4

2

0

DISSOLVED-OXYGEN CONCENTRATION, IN MILLIGRAMS PER LITER

25

20

15

10

5

0

PRODUCTION AND RESPIRATION (grams oxygen/square meter/day)

1200

20

1200

19

1200

18

1200

17

JULY

1200

16

1200

15

1200

14

Clear Creek downstream

Clear Creek upstream

Skull Creek downstream

Skull Creek upstream

Skull Creek gross primary production

Skull Creek respiration

Clear Creek gross primary production

Clear Creek respiration

A.

B.

Best estimate of reaeration

rate coefficient for Skull Creek

Best estimate of reaeration

rate coefficient for Clear Creek

0 0.005 0.010 0.015 0.020 0.025

REAERATION RATE COEFFICIENT (per minute)
10 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

plants, and asynchrony between photosynthesis and metabolic 

costs (Bott and others, 1985).

The SMP uses two methods to calculate daytime respiration (for example, fig. 6). The first method uses the average 

respiration flux of two nighttime periods (see Determination 

of Analysis Period section) to calculate a constant daytime 

respiration rate. The approach can be written as follows:

 Rcon = [(SN1/n1) + (SN2/n2)]/2, 

 

where

Rcon = constant daytime respiration throughout the 

daylight period; 

SN1 = the sum of the net metabolism flux for the 

first nighttime period;

SN2 = the sum of the net metabolism flux for the 

second nighttime period;

n1 = number of individual net metabolism flux 

values during the first nighttime period; 

and

n2 = number of individual net metabolism flux 

values during the second nighttime period.

The daylight respiration rate calculated from eq. 16 is applied 

to each individual time increment during the daylight hours. 

For example, if the measurement interval is 5 min, the daylight 

respiration calculated from eq. 16 is in grams of oxygen per 

5 min, which is applied to each daylight measurement interval.

Mulholland and others (2001) proposed using pre-dawn 

and post-sunset periods for calculating daytime respiration 

in order to reduce errors associated with extrapolation of 

nighttime respiration to daylight conditions. In this approach, 

the average respiration rate is calculated for a 1-hr period 

immediately before dawn; this average rate is assumed to be 

the respiration rate at the beginning of daylight. Similarly, 

an average respiration rate is calculated for the 1-hr period 

immediately following sunset, and this rate is assumed to be 

the respiration rate at the end of daylight. Respiration at each 

measurement interval during daylight then is extrapolated 

between these beginning and ending rates. The approach can 

be written as

 Rvar(t) = Rpre-dawn + [(Rpost-sunset – Rpre-dawn)/(nd –1) * Ni], 

 

where

Rvar(t) = respiration rate at a given time during 

daylight;

Rpre-dawn = the average respiration rate calculated from 

individual net metabolism fluxes for the 

1-hr period immediately before dawn;

Rpost-sunset = the average respiration rate calculated from 

individual net metabolism fluxes for the 

1-hr period following sunset;

nd = the total number of measurement intervals 

during daylight hours, including the first 

and last daylight readings; and

Ni = the serial number of the daylight 

measurement interval for which Rvar(t) is 

calculated, with Ni=1 = 0.

A 24-hr respiration value (grams of oxygen per day) for 

community respiration, Rc, is calculated from the two nighttime periods and the daylight period as follows: 

where

Rd = daytime respiration, in grams of oxygen per 

measurement interval;

Td = duration of the daytime period, in hours;

TN1 = duration of the first nighttime period, in 

hours; and 

TN2 = duration of the second nighttime period, in 

hours.

The first term on the right side of eq. 18 is the summation of 

the incremental daylight respiration values for each measurement interval. The second term on the right side of eq. 18 is 

the sum of the total respiration for the two nighttime periods 

(see eq. 16), adjusted so that the duration of the sum of these 

two periods and the daylight period equals 24 hr. Community 

respiration in eq. 18 is in grams of oxygen per day.

(16)

(17)

In this application, Rvar(t=1) is Rpre-dawn, and Rvar(i=nd) is Rpost-sunset.

=

=

= ++ - + å 1 2 1 2

1

( ) ( )[(24 ) /( )] c d N N dN N

t nd

t

R Rt S S T T T (18)
User’s Guide 11

Gross Primary Production and 

Net Ecosystem Production

Gross primary production for a measurement interval is 

computed as the difference between the net metabolism flux 

and community respiration for the time interval, or

 GPP(t) = NM(t) – Rc(t), 

 

which is a form of eq. 2 and is in grams of oxygen per measurement interval. 

User’s Guide

This section provides step-by-step instructions for 

importing data into the Stream Metabolism Program (SMP), 

completing required data fields, and performing various 

calculations. Guidance is provided first for using the SMP 

to analyze two-station whole-stream metabolism data. The 

differences between application of the SMP for analyzing twostation and single-station data also are presented. Required and 

optional data required to apply the SMP are summarized in 

table 1. 

Two-Station Method

Instructions for completing and executing each page (or 

tab) of the SMP for the two-station whole-stream metabolism 

method are presented below. The active page is indicated 

by the red rectangle around the active tab (see, for example, 

fig. 7). Data used in the example are from Skull Creek near 

Linwood, Nebraska. 

Site Data

Relevant site information is entered on the Site Data page 

(fig. 7). Most of the information on this page is for documentation only and is not used in the calculations. The Metabolism 

Method 2-Station button should be selected (indicated by red 

arrow, fig. 7). Other fields can be populated as desired. The 

fields for Instrument Start Recording Data and Instrument 

Finish Recording Data represent the beginning and ending 

times for data collected by the in situ water-quality meters, 

and the fields are automatically populated by the software after 

the meter data are imported (Meter page). Likewise, the Light 

Meter Number is read from the light meter input file. The 

Instream Meter Recording Interval is the average interval, 

in minutes, between readings at both the upstream and 

downstream meters and is calculated by the SMP after meter 

data are imported. Similarly, the Light Meter Recording 

(19)

Figure 6. Calculated daytime respiration for Athanum Creek at Union Gap, Washington, August 19, 2003.

200

150

100

50

0

-50

-100

-150

-200

-250

-300

OXYGEN FLUX, IN GRAMS OF OXYGEN PER 5-MINUTE MEASUREMENT INTERVAL

0000 0200 0400 0600 0800 1000 1200 1400 1600 1800 2000 2200 0000

August 19, 2003

Net metabolism

Constant daytime respiration

Daytime respiration interpolated from average

pre-dawn and average post-sunset respiration
12 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

Table 1. Required and optional data for the Stream Metabolism Program.

[—, not applicable]

Data Measurement frequency Comments

Required data

Reach length Once —

Travel time through 

the reach

Once, at the same flow for which wholestream metabolism variables are measuredSee Kilpatrick and Wilson (1989). 

Reach-averaged 

wetted width

Once, at approximately the same flow as that 

during the metabolism measurements

See Fitzpatrick and others (1998).

Stream discharge At least once during the time whole-stream 

metabolism variables are measured

Discharge at upstream and downstream ends of the 

reach should be equal, within the limits of 

measurement accuracy.

Dissolved-oxygen 

concentration

Continuously for at least 30 hours and 

including 2 nighttime periods

Pre- and post-deployment calibrations should be 

performed.

Water temperature Concurrent with dissolved-oxygen 

measurements

—

Barometric pressure At the beginning and end of the meter 

deployment

—

Optional data

Photosynthetically 

active radiation 

(PAR)

Continuously during the metabolism 

measurements

Used to automatically establish calculation period 

and to adjust gross primary productivity for PAR.

Reaeration rate 

coefficient

Once, during metabolism study See Kilpatrick and others (1989). Optionally, the 

reaeration rate coefficient can be estimated by 

using one of several empirical relations.

Selected stream 

metrics

Water-surface slope, average depth, velocity 

(calculated as reach length divided by travel 

time) measured once at the same flow as 

metabolism measurements 

These metrics might be needed for use in estimating the reaeration rate coefficient from empirical 

equations.
User’s Guide 13

Interval is the average time, in minutes, between light meter 

readings during the deployment and is calculated by the SMP 

after meter data are imported.

The DO concentration from independent DO measurements that are performed during the data-collection period 

should be entered in the Field DO Verification fields 

(indicated by yellow arrow, fig. 7), along with the time the 

measurements were made. Fields are available for measurements made at the upstream and downstream ends of the study 

reach and at the beginning and end of the deployment. 

In order to determine if the streamflow at the start and 

end of the deployment are the same, water-surface elevation 

measurements are often made by measuring down to the water 

surface from a fixed point. These measurements are noted 

in the Water-surface elevation referenced to arbitrary 

datum fields, with the first value entered in the left-most field 

(indicated by blue arrow, fig. 7) being the measurement at the 

upstream end of the reach at the beginning of the deployment. 

Complete dates and times (for example, “7/18/2003 12:05 

PM”) of independent DO measurements and water-surface 

elevation measurements can be entered in the appropriate 

fields, although the size of the fields on the Site Data page do 

not permit full display of the date and time values. Information 

on this page should be supplemented by complete field notes. 

Stream Metrics

The Stream Metrics page (fig. 8) contains information on 

hydrologic and physical conditions in the study reach. Some 

of the data are needed to perform other calculations. All units 

on this page (and others) are metric. Fields on the Stream 

Metrics page are populated with default values when the page 

is first opened, but these default values should be replaced 

with measured information. Data entered on this page include 

the following:

•	 Reach Length (in meters) is needed to calculate the 

channel wetted area, which is used to determine production per unit area. Channel wetted area is calculated 

as the reach length multiplied by the reach-averaged 

wetted width.

•	 Travel Time (in minutes) is required in the calculation 

of reach-averaged T, DO, and DOs and may be required 

for some forms of empirical equations used to estimate 

the reaeration rate coefficient. The meter-recording 

interval should be less than the travel time through the 

reach.

Figure 7. Screen capture of the Site Data page in the Stream Metabolism Program.
14 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

•	 Ave. Velocity (in meters per second), or average 

stream velocity, may be required for some forms of 

the empirical equations used to estimate the reaeration 

rate coefficient. Average velocity should be determined 

from the reach length divided by the travel time. This 

value is not required and is not used by the SMP.

•	 Reach Ave. Wetted Width (in meters), or reachaveraged wetted stream width, is needed to calculate 

the channel wetted area, which is used to determine 

production per unit area and may be required for some 

forms of the empirical equations used to estimate the 

reaeration rate coefficient. Average width should be 

determined from detailed morphometric measurements 

made at the site (for example, Fitzpatrick and others, 

1998).

•	 Reach Ave. Depth (in meters), or reach-averaged water 

depth, may be needed for some forms of the empirical 

equations used to estimate the reaeration rate coefficient. This value is not required and is not used by the 

SMP.

•	 Slope (meter/meter) is the water-surface slope measured over the study reach and may be required for 

some forms of the empirical equations used to estimate the reaeration rate coefficient. This value is not 

required by the SMP.

•	 Flow (in liters per second) is the stream discharge 

that is determined from measurements made at the 

site. It often is appropriate to measure discharge at the 

upstream and downstream ends of the study reach to 

determine if ground water is discharging to the stream 

or if the stream is losing flow in the reach. Ideally, flow 

is steady throughout the study period.

•	 Barometric Pressure (reported in millimeters of mercury [mm Hg]) is needed to calculate DOs

 (see eq. 8). 

The barometric pressure is assumed to be constant 

throughout the deployment, including the pre- and 

post-calibration period. The mean barometric pressure 

determined from readings when meters are deployed 

and when meters are recovered is an appropriate value 

to enter in this field.

•	 Meter Measurement Interval (in minutes) is the time 

interval at which the in situ water-quality meter was 

pre-set to collect data. The exact measurement interval 

for both the in situ water-quality meters and the light 

meter are calculated by the SMP, and the appropriate 

fields are populated automatically on the Site Data

page (fig. 7) after the meter data have been imported 

into the SMP.

•	 Light Meter Measurement Offset (in minutes) is 

populated only if the light meter and the water-quality 

meters were not set at exactly the same clock time. For 

Figure 8. Screen capture of the Stream Metrics page in the Stream Metabolism Program.
User’s Guide 15

example, if the water-quality meters were set at standard time and the light meter was set at daylight-saving 

time, the offset will be –60 to correct the light meter to 

standard time. If there is no offset, the field can be left 

blank.

•	 Reaeration Coefficient, or K2, can be estimated from 

available empirical equations or determined from 

tracer-gas tests at the study site (for example, Kilpatrick and others, 1989). Empirical equations for predicting K2 were reviewed by Rathbun (1977), Gromiec 

(1989), and Moog and Jirka (1998), and numerous 

others. The reaeration rate coefficient is reported in 

min–1, and empirically estimated values of K2 should 

be corrected to 20 oC (Elmore and West, 1961; eq. 15). 

Most empirical equations, however, provide estimates 

of K2 at 20 oC, so no conversion is needed. If the 

reaeration rate coefficient is determined from tracergas measurements, the water temperature at which the 

measurements were made is entered (indicated by red 

arrow, fig. 8), and the SMP will adjust the measured 

K2 to the water temperature during the metabolism 

measurements. 

Meter—Importing Data 

Two time-series of water-quality (DO, T, pH, and SC) 

data are imported into the SMP on the Meter page (fig. 9). 

As an option, a single time series of PAR data also can be 

imported on the Meter page. Data are synchronized in time on 

the Meter page, and corrections for DO sensor error and drift 

are determined.

Water-quality data files must be comma delimited and 

have the format shown in figure 10. The maximum number of 

lines of data that can be imported into the SMP is 64,000.

The first two lines in the water-quality data files are the 

same for every in situ meter data file that is imported and 

should be exactly like the first two lines in figure 10. The 

first line of the data file provides the name of each parameter 

in the data file, with the name enclosed by double quotation 

marks. The parameters are date, time (24-hr clock), water 

temperature, specific conductance, DO concentration, DO 

sensor charge (a troubleshooting parameter available on some 

in situ water-quality meters), pH, and pH sensor voltage (also 

a troubleshooting parameter available on some in situ waterquality meters). The second line of the data file gives the units 

in which each parameter is reported: date, in month/day/year; 

time, in hours:minutes:seconds; water temperature, in degrees 

Figure 9. Screen capture of the unpopulated Meter page in the Stream Metabolism Program.
16 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

Celsius; specific conductance, in millisiemens per centimeter; 

DO concentration, in milligrams per liter; DO sensor charge, 

dimensionless; pH, in standard units; and pH sensor voltage, 

in millivolts. The remaining lines are the data in the same 

order given on the first line of the file. Date and time are 

always enclosed by double quotation marks. The only readings 

that are required by the SMP are date, time, water temperature, 

specific conductance, and DO. If the other parameters are 

unavailable, a zero can be entered in the appropriate field 

of the data file. For example, if only the required data were 

available, the first line of data in figure 10 would be:

"08/18/03","15:40:39",23.89,0.001,8.28,0,0,0

The file format shown in figure 10 is produced by YSI 

Environmental’s EcoWatch® for Windows® software when 

using data from YSI multiparameter instruments. Data files 

from any source, however, can be processed by the SMP as 

long as the files have the format shown in figure 10. Simple 

scripts can be written, for example, to convert data files from 

other multiparameter water-quality meters to the format 

required by the SMP.

Water-quality meter data are imported by clicking the 

Read DO Meter Text File button (indicated by red arrow, 

fig. 11). A Windows Explorer® window will appear, allowing 

the user to browse to the directory containing water-quality 

monitoring data. Select the data file from upstream meter 

Figure 10. Example of text file format required for importing water-quality data into 

the Stream Metabolism Program.

Figure 11. Screen capture of the Meter page populated with data from upstream and downstream waterquality meters, and prior to importing light-meter data, in the Stream Metabolism Program.

"Date","Time","Temp","SpCond","DO Conc","DO Charge","pH","pHmV"

"M/D/Y","hh:mm:ss","C","mS/cm","mg/L","","","mV"

"07/18/03","11:30:40",26.82,0.007,7.68,45,9.46,-160.9

"07/18/03","11:35:39",26.83,0.006,7.62,45,9.47,-161.7

"07/18/03","11:40:39",26.85,0.006,7.59,45,9.48,-162.3

"07/18/03","11:45:39",26.90,0.005,7.56,45,9.49,-162.7
User’s Guide 17

first, then select the downstream data file. After both files are 

selected, the data table will be populated (fig. 11).

Several pieces of information are produced automatically 

after the in situ meter data are imported (compare figs. 10 and 

11). The path name from which the in situ meter data were 

read is documented (indicated by blue arrow, fig. 11). The 

number of rows in the spreadsheet (or Data Points Sampled), 

the total time of data collection (Duration), and the average 

interval, in minutes, between in situ meter readings (Ave. 

Interval) are all reported (fig. 11, green box). In this example 

(fig. 11), the spreadsheet contains 614 values, and data were 

collected for 2 d, 3 hr, and 5 min.

As discussed previously, several fields on the Site Data

page (fig. 7) are automatically populated when the in situ 

meter data are imported. Other features of the Meter page 

include the following:

•	 The first data value is assigned a record number 

(Rec#) of “0” (fig. 11, left-most column).

•	 Column widths can be changed by dragging the cell 

boundary for the title cell (indicated by red arrow, 

fig. 12). Note that the fields for US Water Temp. 

(upstream water temperature) and US Sp Cond.

(upstream specific conductance) contain the complete column titles when cell widths are increased 

(compare figs. 11 and 12). The size of the entire 

window, however, cannot be changed, so the bottom 

scroll bar (highlighted in yellow, fig. 11) must be 

used to view all of the columns. Likewise, the scroll 

bar to the right of the window (highlighted in yellow, 

fig. 11) can be used to scroll through the rows of 

data.

•	 All columns for water-quality monitoring data are 

populated even if no data were collected. In the 

example shown in figure 13, recording at the downstream meter was stopped while the upstream meter 

continued to record for 30 additional min. A DS 

Date/Time value of “1/1/0001 12:00:00” (fig. 13, 

green box) is assigned if no data were collected at 

one meter but were collected at the companion site. 

Such an occurrence could be at the beginning or the 

end of the data-collection period.

•	 Data cannot be edited on the Meter page. Any 

changes in the data must be made in the raw data file 

before the data are imported to the SMP. 

•	 Data can be exported from the Meter page by selecting a single or multiple rows of data. The cursor 

is placed on the cell to the left of Rec# on the first 

row of data to be selected (red arrow at Rec# 0001 

in fig. 14) and dragged to the last record number to 

be selected (Rec# 0007 in fig. 14). Selected rows 

are highlighted in blue (fig. 14). Then, by using the 

keyboard command Ctrl-C, the selected rows can be 

pasted into a spreadsheet. Data cannot, however, be 

copied from a spreadsheet back into the Meter page. 

Rows can be unselected by clicking the Unselect All 

Records button (yellow arrow, fig. 14).

Figure 12. Screen capture of a section of Meter page in the Stream Metabolism 

Program showing a boundary that can be dragged to expand column width and 

full column headings for upstream water temperature and upstream specific 

conductance data.
18 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

Figure 13. Screen capture of a Meter page in the Stream Metabolism Program showing condition in which 

data were collected at only one of the two in situ water-quality meters for a portion of the deployment period.

Figure 14. Screen capture of the Meter page in the Stream Metabolism Program showing rows selected 

for copying into a spreadsheet application.
User’s Guide 19

Light data from a single site can be imported into the 

SMP, but these data are not required. If light data are imported, 

however, they must be in the format shown in figure 15. 

These data were collected by Onset Computer Corporation’s 

HOBO® data loggers, and data files were downloaded and 

processed into tab-delimited ASCII text files using Onset’s 

BoxCar Pro 4®. The first line of the light-data file identifies 

header information and includes the instrument identification 

number (in this case, #672162). The remaining lines list 

the data, which include the date (month/day/year), time 

(hour:minute:seconds), and PAR values in micromoles per 

square meter per second [μmol/(m2/s)]. Light-data files from 

any source can be imported into the SMP as long as the file 

format is the same as shown in figure 15. 

have been imported. As with the water-quality data, the user is 

prompted to browse to the directory with light data and select 

a data file to import. After light data have been added to the 

data table (indicated by yellow arrow, fig. 16), the Read Light 

Text File button is no longer highlighted.

The following data columns are on the Meter page (from 

left to right):

•	 The record number, with the first record number being 

“0;”

•	 Date and time when upstream meter reading was made;

•	 Upstream meter water temperature (oC);

•	 Upstream meter specific conductance (mS/cm);

•	 Upstream meter DO concentration (mg/L);

•	 Upstream meter pH (standard units);

•	 Upstream meter measurement interval 

(hours:minutes:seconds);

•	 Date and time when downstream meter reading was 

made;

•	 Downstream meter water temperature (oC);

•	 Downstream meter specific conductance (mS/cm);

•	 Downstream meter DO concentration (mg/L);

•	 Downstream meter pH (standard units);

•	 Downstream meter measurement interval 

(hours:minutes:seconds);

Figure 15. Example of file format required for importing 

light-meter data into the Stream Metabolism Program.

Figure 16. Screen capture of the Meter page in the Stream Metabolism Program populated with waterquality monitoring data and light-meter data.

Date Time PAR [μmol/(m2/s)] 

#672162

08/18/03 16:00:42.0 53.8

08/18/03 16:15:42.0 66.3

08/18/03 16:30:42.0 63.8

Light data are imported by clicking the Read Light Text 

File button (blue outline, fig. 16). The Read Light Text File

button will be visible only after water-quality monitoring data 
20 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

•	 Date and time when light meter reading was made;

•	 Light meter reading [μmol/(m2/s)];

•	 An index (“Night to Day”) for the beginning and ending (“Day to Night”) of daylight. Daylight is assumed 

to end when PAR becomes less than 2 μmol/(m2/s) and 

is assumed to begin when PAR exceeds 2 μmol/(m2/s) 

(indicated by red arrow, fig. 16; also see fig. 3).

Meter —Calculation of Dissolved-Oxygen 

Adjustments 

Adjustments to DO readings are calculated on the Meter

page. Adjustments may be required because of inadequate 

meter calibration, sensor drift, and fouling during deployment. 

The adjustments can be calculated automatically or directly. 

Direct adjustments may be required if the barometric pressures 

at the beginning and end of the deployment are markedly 

different.

Adjustments to DO readings are calculated by using 

data from the pre-deployment and post-deployment periods 

when DO in saturated air is recorded. The text boxes on the 

bottom right of the Meter page (for example, fig. 17) should 

be completed. Record numbers (Rec#) are entered in the boxes 

corresponding to the time when the pre-calibration period 

began and the time when the pre-calibration period ended. The 

pre-calibration period is on the left (see red outlined Begin, 

fig. 17), and the post-calibration period is on the right (see 

red outlined End, fig. 17). In this case, pre-calibration of the 

upstream meter (fig. 11) began at 11:35 AM on July 18 

(Rec# = 1) and ended at 11:55 AM (Rec# = 5). The precalibration period for the downstream meter also began at 

11:35 AM (Rec# = 1) but ended at 11:45 AM (Rec# = 3).

The pre- and post-calibration periods can be identified in 

two ways. The first way is to refer to field notes. The second 

way the pre- and post-calibration periods can be identified is 

to review the data in the spreadsheet. Specific conductance 

during calibration in saturated air should be near zero. So 

in the example in figure 11, specific conductance for the 

upstream meter was between 0.005 and 0.009 mS/cm for 

the first five readings in saturated air and increased to 

0.573 mS/cm after the meter was placed in the stream. 

Temperature fluctuations should be small during the preand post-deployment calibration periods. In fact, it is possible 

that record number 5 for the upstream meter should not be 

used in the drift calculation because the temperature increased 

almost 1 oC, and the specific conductance almost doubled 

between 11:50 and 11:55, indicating some disturbance to the 

meter. The first readings (record number 0) were not used in 

order to ensure stability of the sensors. 

The pre- and post-calibration periods should be no longer 

than 1 hour, even if calibration data were recorded for longer 

than 1 hr. The period (no more than 1 hr) immediately prior to 

and immediately after deployment should be used for the drift 

calculations.

The blue values shown in figure 17 are the result of 

clicking the Calculate Drift button after the appropriate 

record numbers have been entered in the text boxes. The 

Calcd. Drift values represent the average error, in milligrams 

per liter, for each period (pre- and post-deployment) and meter 

(upstream and downstream). For example, the average initial 

error for the upstream meter during the pre-calibration period 

(fig. 17) was 0.36 mg/L (meter was reading lower than correct 

values), and the average error for the upstream meter during 

the post-calibration period was 0.40 mg/L. Consequently, 

the drift during the deployment was 0.04 mg/L. The section 

on theoretical basis for calculations describes the internal 

procedures used to correct the measured DO data for initial 

error and drift.

In some cases, calculated net ecosystem production 

(NEP) can be sensitive to the DO values used in the drift 

calculations. Such effects on NEP of the DO readings used in 

the drift calculations should be carefully evaluated, particularly if there is some uncertainty about the appropriate record 

numbers to be used in the calculations (for example, record 

number 5 for the upstream meter beginning error, as discussed 

above).

Adjustments to DO readings for initial error and drift can 

be entered manually by clicking the Input Drift button (blue 

outline, fig. 17), which results in the pop-up window shown 

in figure 18. The text boxes then can be completed with the 

appropriate values. Recall that the error is positive if the meter 

reading is less than the actual DO concentration in saturated 

air. If the automated drift calculation is not used, zero values 

should be entered into the record number fields (fig. 17) in the 

Meter Drift section of the Meter page. 

Figure 17. Screen capture of the Meter Drift section of the Meter page used 

for dissolved-oxygen sensor drift calibration in the Stream Metabolism Program.
User’s Guide 21

Graph Meter Data—Automated Selection of 

Analysis Period 

Water temperature, DO concentration, and PAR are 

automatically plotted against time (horizontal axis) on the 

Graph Meter Data page after data are imported (fig. 19). Data 

are not plotted to scale. Rather, the plots are given for a quick 

visual inspection to ensure that the data sets do not include any 

obvious outliers. Yellow bars are PAR, the red line is water 

temperature, and the white (or gray) line is DO.

The analysis period is selected automatically (also see 

fig. 16) and is shown on the Graph Meter Data page (fig. 19). 

The vertical white lines (adjacent to white arrows) depict 

the beginning (left) and end (right) of the daylight period, 

respectively. The vertical blue lines (adjacent to blue arrows) 

depict the beginning (left) and end (right) of the analysis 

period, respectively. These periods (daylight and analysis) also 

are depicted in figure 3, which depicts values plotted to scale. 

Information regarding the various components of the analysis 

period are shown at the lower left side of the Graph Meter 

Data page (green outline, fig. 19). The components of the 

analysis period are described in the Theoretical Background

section of this report. The information contained under the 

heading “Gross Primary Production Calculation Periods” 

(green outline, fig. 19) is as follows, starting with the column 

on the left, from top to bottom:

•	 Day Start

•	 Night Start: The value within the field (outlined in 

blue) is the number of hours from the beginning of 

daylight when the first nighttime period begins. A 

Figure 18. Screen capture of the Instrument Drift window 

for entering beginning and ending errors in dissolvedoxygen meter readings in the Stream Metabolism Program.

Figure 19. Automatically graphed data showing time-series plots of dissolved-oxygen 

concentration, water temperature, and photosynthetically active radiation, though not to scale, 

and identified gross primary production calculation periods, as a feature of the Stream Metabolism 

Program.
22 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

negative value indicates hours before the beginning 

of daylight period. Adjacent to this field is the date 

and time (outlined in red) of the beginning of the 

first nighttime period.

•	 Night End: The first nighttime period ends 1 hr plus 

one water-quality meter reading before the beginning 

of daylight. The value within the field is the number of hours from the beginning of daylight when 

the first nighttime period ends. As before, a negative value indicates a time before the beginning of 

daylight period. Adjacent to this field is the date and 

time of the end of the first nighttime period. In the 

example, the measurement interval is 5 min, so the 

first nighttime period ends at 5:35 AM, or 65 minutes before the beginning of daylight at 6:40 AM.

•	 Pre Dawn Start: The pre-dawn period is always 1 hr 

long and always begins 1 hr before the beginning of 

daylight, as indicated by the –1.0 in the example data 

field (fig. 19). Adjacent to the field is the date and 

time of the beginning of the pre-dawn period. 

•	 Pre Dawn End: The end of the pre-dawn period 

is one water-quality meter measurement interval 

before the beginning of daylight; in the example, the 

measurement interval is 5 min and daylight begins at 

6:40 AM, so the pre-dawn period ends at 6:35 AM.

•	 Values in the right column under the heading “Gross 

Primary Production Calculation Periods” have meanings analogous to those in the left column, except 

these values are for the end of daylight, the postsunset period, and the second nighttime period.

Meter and Graph Meter Data—Manual 

Selection of Analysis Period 

After the light-meter data are imported, the SMP 

automatically selects the first full day of data for analysis. The 

daylight period selected for analysis is highlighted in blue on 

the Meter page (fig. 16) and is shown on the Graph Meter 

Data (fig. 19) page as previously described. Users may choose 

to manually select the analysis period for certain cases, such 

as when multiple days of data are available or when PAR readings are unavailable. The user can override the automatically 

selected analysis period in one of two ways. The steps for the 

first approach are as follows:

1. Click Unselect All Records on the Meter page (green 

outline, fig. 16). The rows that were previously highlighted in blue (fig. 16) will no longer be highlighted, and 

the vertical white lines on the Graph Meter Data page 

(fig. 19) will disappear.

2. Review the data on the Meter page and select a daylight 

beginning time on the day when the analysis is to be 

performed. If PAR data are available, this typically will 

be the time corresponding to the first PAR value greater 

than 2 μmol/(m2/s). For the purposes of this example, it is 

assumed that no PAR data are available and that published 

values of sunrise and sunset are used to identify daylight 

beginning and end times.

3. Click the cell in the left column on the Meter page corresponding to the selected time (fig. 20, red arrow). The 

selected row is highlighted in blue.

4. Scroll down the table and locate the daylight ending time. 

Again, if PAR data are available, this typically will be the 

time corresponding to the last PAR value for the day with 

a value greater than 2 μmol/(m2/s). Click on the cell of the 

corresponding row of the left column while holding down 

the Shift key. The entire daylight period will be highlighted in blue, and the two vertical lines on the Graph 

Meter Data page are re-plotted for the new daylight 

period (fig. 21). For the purposes of this example, daylight 

is assumed to begin at 6:30 AM and end at 9:00 PM.

5. Although the daylight period is indicated on the Graph 

Meter Data page, the beginning of the first nighttime 

period and end of the second nighttime period and the 

correct clock times are not shown on this page (fig. 21). In 

order to complete selection of the analysis period, click on 

the button User types processing period offsets in boxes 

found (blue outline, fig. 22). After this button is clicked, 

the fields for Night Start and Night End become active. 

Backspace over the default value, enter the desired value, 

and click the Tab button. At this point, all of the dates and 

clock times on the page accurately reflect the components 

of the analysis periods, and the blue vertical lines representing the beginning and end of the analysis period are 

shown on the graph (fig. 23).

The analysis period also can be set graphically as follows:

1. Repeat previous step 1.

2. Click Enable Graphic Selection (green outline, fig. 24).

3. Click Start Time button (red arrow, fig. 24).

4. Click in the plot window at the desired starting time 

(white arrow, fig. 24). The Day Start (or beginning of 

daylight) time is then displayed. The beginning of daylight time can be adjusted by continuing to click in the 

plot window until the desired time is selected.

5. Repeat steps 3 and 4 for the end of daylight (Ending

Time). After the ending time is selected, the beginning of 

the first nighttime period and the end of the second nighttime period (vertical blue lines, fig. 23) also are shown, 

along with the beginning and end of daylight (vertical 

white lines, fig. 23). 

6. Uncheck the Enable Graphic Selection box.

7. Nighttime beginning and end times can be adjusted as 

previously described.
User’s Guide 23

Figure 20. Screen capture of the Meter page showing user-selected daylight beginning time 

in the Stream Metabolism Program.

Figure 21. Automatically re-graphed data after manually selecting a daylight period in the Stream 

Metabolism Program.
24 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

Figure 22. Screen capture of the Graph Meter Data page showing manually entered nighttime periods 

in the Stream Metabolism Program.

Figure 23. Screen capture of the Graph Meter Data page following manual entry of all analysis period 

information in the Stream Metabolism Program.
User’s Guide 25

Calculate Metabolism

The next step is to calculate the various metabolism 

measures, which is done by clicking the “Calculate Metabolism” button on the Calculate Metabolism page (green outline, 

fig. 25). If the instrument drift has not been entered or calculated (figs. 17, 18), a pop-up window is displayed reminding 

the user to perform this operation before the metabolism 

measures can be calculated. Calculated Metabolism Values

(white arrow, fig. 25) can be exported to an Excel® spreadsheet 

by clicking the Write to Excel button (yellow outline, fig. 25). 

This process is somewhat slow and can take as long as 

20–30 seconds to complete. An Excel® window opens when 

the process is completed.

Calculated values for each time step are given on the 

Calculate Metabolism page (fig. 25). These same values 

are the values exported to the Excel® spreadsheet; measured 

values also are exported to the spreadsheet. The variables on 

the Calculate Metabolism page are as follows:

•	 Rec#, the record number;

•	 Date Time, the date and time of observation;

•	 US DO Corr. (mg/L), the DO concentration at the 

upstream meter, corrected for instrument error and 

drift [Note that the first value is for record number 

6 (blue arrow, fig. 25). Recall that record numbers 1–5 were used to calculate the drift and error 

(fig. 17). The initial error for the upstream meter was 

0.36 mg/L (fig. 17), and the instrument reading was 

7.70 mg/L (fig. 11). Hence, the corrected reading 

for record number 6 is (7.70 + 0.36) = 8.06 mg/L 

(eq. 9; fig. 25). All subsequent calculations, with one 

exception described later, are based on the corrected 

DO values.];

•	 DS DO Corr. (mg/L), DO concentration at the 

downstream meter, corrected for instrument error 

and drift; 

•	 US DO Sat. (mg/L), DO saturation concentration at 

the upstream meter; 

•	 DS DO Sat. (mg/L), DO saturation concentration at 

the downstream meter; 

•	 Ave Reach Temp (oC), reach-averaged water temperature, calculated by using eq. 11 [In this example, 

the travel time through the reach is 85 min, so the 

first reach-averaged temperature is calculated 85 min 

(or at 1:25 PM) after the temperature reading corresponding to the first DO reading at 12:00 PM (blue 

arrows, figs. 25, 26).];

Figure 24. Screen capture of the Graph Meter Data page showing graphical selection of the 

beginning of the daylight period for graphical analysis in the Stream Metabolism Program.
26 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

Figure 25. Screen capture of the Calculate Metabolism page in the Stream Metabolism Program.

Figure 26. Screen capture of the Calculate Metabolism page showing reach-averaged calculations in 

the Stream Metabolism Program.
User’s Guide 27

•	 US DO Deficit (mg/L), DO deficit (DOs – DO) at 

upstream meter;

•	 DS DO Deficit (mg/L), DO deficit at downstream 

meter;

•	 Ave DO Def. Reach (mg/L), reach-averaged DO 

deficit;

•	 DO Diff. Reach (mg/L), the difference between the 

downstream DO and the upstream DO, offset by the 

travel time (the term in brackets in eq. 15);

•	 Reaeration Flux (mg/min), value calculated using 

eq. 12;

•	 Metabolism Flux (mg/min), value calculated using 

eq. 15;

•	 GPP Flux (mg/min), gross primary productivity 

calculated from eq. 19; values are reported for the 

daylight period; and

•	 Extrapolated Daytime Respiration (mg/min), respiration for the measurement interval calculated from 

eq. 17; values are reported for the daylight period. 

A summary of respiration values during various time 

periods also are reported on the Calculate Metabolism page. 

All of the reported values are average respiration rates, in 

grams of oxygen per square meter per recording interval. 

Total respiration for a particular period can be calculated by 

multiplying the value reported on this page by the recording 

interval (5 min for this example). First night R is the average 

respiration rate from the beginning of the first nighttime period 

until 1 hr before daylight, or in this example, from 11:35 PM 

on July 18 until 5:35 AM on July 19 (fig. 19). Second night 

R is calculated similarly for the second nighttime period. Ave 

Pre Dawn R and Ave Post Sunset R are the average respiration rates for the 1-hr period before dawn and the 1-hr period 

after sunset, respectively. The Ave Daytime R is calculated 

from the daylight respiration values interpolated between the 

average pre-dawn R and and average post-sunset R. 

Summary Output 

Information on the Summary Output page is generated 

when the “Calculate Metabolism” button (green outline, 

fig. 25) is clicked. Input values from the Stream Metrics page 

are summarized along with the calculated reach wetted area 

on the Summary Output page (blue outline, fig. 27). The 

next group of variables is related to daylight and PAR (green 

outline, fig. 27). The Total daylight PAR is calculated by 

summing the PAR values (in micromoles per square meter 

per second) for the daylight period, and multiplying the sum 

by the number of seconds in the PAR measurement interval. 

Maximum Daily PAR is the highest instantaneous PAR reading during the daylight period, and Average Daylight PAR is 

the Total daylight PAR divided by the Daylight length.

Figure 27. Screen capture of the Summary Output page in the Stream Metabolism Program.
28 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

Some general statistics on DO and water temperature also 

are summarized on the Summary Output page (yellow outline, 

fig. 27). “US” indicates the upstream monitoring location, and 

“DS” is the downstream site. The “average” values are for the 

daylight period, and the “maximum” and “minimum” values 

are for the calendar date for which metabolism variables are 

calculated; in this example, July 19, 2003.

The maximum and minimum rate of change in DO 

concentration also can be calculated on the Summary Output 

page. The interval (in minutes) over which the rate of change 

is to be calculated is entered in the field adjacent to Maximum 

Rates Calculation Time Period (mins) (blue underline, 

fig. 27), and the Calculate Maximum Rates button is clicked. 

Maximum production rate is the largest positive rate, 

given in milligrams per liter per minute, and the Maximum 

respiration rate is the largest negative rate. The time associated with the maximum and minimum rates is the beginning 

of the period with the largest rate. For example, the period 

with the maximum production rate is between 10:35 AM 

and 12:35 PM, because the rate was calculated for a 120-min 

period. These rates are calculated using uncorrected DO data 

from the upstream station.

Information on the Summary Output page can be written 

to a text file. Data are comma delimited and written on one 

continuous line. This approach is advantageous when data 

from multiple sites are analyzed, so that the text file can be 

imported to a spreadsheet.

Data Archive

The Data Archive page (fig. 28) contains information 

that is useful primarily to those involved in modifying the 

program code. The page does, however, contain one important 

feature—the Save Current Setup to Text File button (blue 

outline, fig. 28), which allows the user to save all of the work 

that has been completed, including information from each of 

the other pages in the SMP. In a subsequent session, the user 

can open the software, click on the Data Archive tab, and 

then click on the Read Saved .txt File button (blue outline, 

fig. 29), browse the directory in which the saved setup file 

is located (default file name is setup.txt), and import the file 

into the SMP. Everything from the previous session will be 

restored with one exception. The metabolism calculations 

from the previous session will not be restored, so the user 

must again click on the Calculate Metabolism button (green 

outline, fig. 25) on the Calculate Metabolism page.

Single-Station Method

The SMP can be used with single-station data to compute 

a subset of the variables computed using the two-station 

method. The approach for the single-station method is 

generally the same as for the two-station; only the differences 

between the two methods will be highlighted here.

Figure 28. Screen capture of the populated Data Archive page in the Stream Metabolism Program.
User’s Guide 29

The only differences between single- and two-station 

applications on the Site Data page are (1) the “1-Station” 

method is selected (blue arrow, fig. 30), and (2) data for 

only one set of readings are entered. Most of the fields on 

the Stream Metrics page are not active for the single-station 

application (fig. 31); only information on flow, barometric 

pressure, recording interval, and meter offset are required.

Single-station information is entered into the Meter 

page in the same way as the two-station information (fig. 32), 

except the software only accepts data from one recording 

Figure 29. Screen capture of an unpopulated Data Archive page in the Stream Metabolism Program.

Figure 30. Screen capture of the Site Data page for single-station application in the Stream 

Metabolism Program.
30 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

Figure 31. Screen capture of the Stream Metrics page for single-station application in the Stream 

Metabolism Program.

Figure 32. Screen capture of the Meter page for single-station application in the Stream 

Metabolism Program.
User’s Guide 31

meter. Light data may or may not be entered, just as with the 

two-station method. Meter drift calculations are performed 

similarly to the two-station application. The analysis period 

can be selected automatically, as before, or manually on the 

Graph Meter Data page. 

In some studies (for example, Mulholland and others, 

2005), assumptions are made about the length of the reach 

over which the single-station measurement is applicable, 

and metabolism variables then can be calculated. Other 

applications of the single-station method (Wilcock and others, 

1998) report the maximum rate of DO change and compute 

metabolism variables using a steady-state flow model. The 

approach used here is to make no assumptions about the length 

of the stream reach for which the single-station measurement 

applies but rather to report the calculations based only on 

the measurements. As a result, information on the Calculate 

Metabolism (fig. 33) and Summary Output (fig. 34) pages is 

fairly limited, with the primary result being the maximum and 

minimum rate of change in DO concentration.

Figure 33. Screen capture of the Calculate Metabolism page for single-station application in the 

Stream Metabolism Program.
32 Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User’s Guide

References

Bolton, D., 1980, The computation of equivalent potential temperature: Monthly Weather Review, v. 108, 

p.1046–1053.

Bott, T.L., 2006, Primary productivity and community respiration, in Hauer, F.R., and Lamberti, G.A., eds., Methods in stream ecology: San Diego, Academic Press, Inc., 

p. 533–556.

Bott, T.L., Brock, J.T., Dunn, C.S., Naiman, R.J., Ovink, R.W., 

and Petersen, R.C., 1985, Benthic community metabolism 

in four temperate stream systems—An inter-biome comparison and evaluation of the river continuum concept: Hydrobiologia, v. 123, p. 3–45.

Elmore, H.L., and West, W.F., 1961, Effect of water temperature on stream reaeration: Journal of the Sanitary Engineering Division, v. 87, p. 59–71.

Erdmann, J.B., 1979, Systematic diurnal curve analysis: Journal of the Water Pollution Control Federation, v. 15, no. 1, 

p. 78–86.

Fitzpatrick, F.A., Waite, I.R., D’Arconte, P.J., Meador, M.R., 

Maupin, M.A., and Gurtz, M.E., 1998, Revised methods for 

characterizing stream habitat in the National Water-Quality 

Assessment Program: U.S. Geological Survey WaterResources Investigations Report 98-4052, 67 p.

Gromiec, M.J., 1989, Reaeration, in Jorgensen, S.E., and 

Gromiec, M.J., eds., Mathematical submodels in water 

quality systems: Amsterdam, Elsevier Science Publishers, 

Developments in Environmental Modelling, v. 14, p. 33–64.

Hauer, F.R., and Lamberti, G.A., eds., 2006, Methods in 

stream ecology: San Diego, Academic Press, Inc., 877 p.

Kilpatrick, F.A., Rathbun, R.E., Yotsukura, N., Parker, 

G.W., and DeLong, L.L., 1989, Determination of stream 

reaeration coefficients by use of tracers: Techniques of 

Water-Resources Investigations of the U.S. Geological Survey, book 3, chap. A18, 52 p.

Kilpatrick, F.A., and Wilson, J.F., Jr., 1989, Measurement 

of time of travel in streams by dye tracing: Techniques of 

Water-Resources Investigations of the U.S. Geological Survey, book 3, chap. A9, 27 p.

Lewis, E.L., 1980, The Practical Salinity Scale 1978 and its 

antecedents: IEEE Journal of Oceanic Engineering, v. OE-5, 

no. 1, p. 3–8.

Marzolf, E.R., Mulholland, P.J., and Steinman, A.D., 1994, 

Improvements to the diurnal upstream-downstream dissolved oxygen change technique for determining wholestream metabolism in small streams: Canadian Journal of 

Fisheries and Aquatic Science, v. 51, p. 1591–1599.

Figure 34. Screen capture of the Summary Output page for single-station application in the Stream 

Metabolism Program.
References 33

Moog, D.B., and Jirka, G.H., 1998, Analysis of reaeration 

equations using mean multiplicative error: Journal of Environmental Engineering, v. 124, no. 2, p. 104–110.

Mulholland, P.J., Fellows, C.S., Tank, J.L, Grimms, N.B., 

Webster, J.R., Hamilton, S.K., Marti, E., Ashkenas, L., 

Bowden, W.B., Dodds, W.K., McDowell, W.H., Paul, M.J., 

and Peterson, B.J., 2001, Inter-biome comparison of factors 

controlling stream metabolism: Freshwater Biology, v. 46, 

p. 1503–1517.

Mulholland, P.J., Houser, J.N., and Maloney, K.O., 2005, 

Stream diurnal dissolved oxygen profiles as indicators of instream metabolism and disturbance effects—Fort Benning 

as a case study: Ecological Indicators, v. 5, p. 243–252.

Munn, M.D., and Hamilton, P.A., 2003, New studies initiated 

by the U.S. Geological Survey—Effects of nutrient enrichment on stream ecosystems: U.S. Geological Survey Fact 

Sheet 118-03, 4 p.; accessed May 22, 2006, at http://

pubs.usgs.gov/fs/fs11803/

Odum, H.T., 1956, Primary production in flowing waters: 

Limnology and Oceanography, v. 1, p. 102–117.

Ramaswami, A., Milford, J.B., and Small, M.J., 2005, Integrated environmental modeling: New York, John Wiley & 

Sons, Inc., 688 p.

Rathbun, R.E., 1977, Reaeration coefficients of streams—

state-of-the-art: Journal of the Hydraulics Division, v. 103, 

no. 4, p. 409–424.

Rathbun, R.E., Stephens, D.W., Shultz, D.J., and Tai, D.Y., 

1978, Laboratory studies of gas tracers for reaeration: 

Journal of the Environmental Engineering Division, v. 104, 

no. 2, p. 215–229. 

Tsivoglou, E.C., Cohen, J.B., Shearer, S.D., and Godsil, P.J., 

1968, Tracer measurements of stream reaeration: II. Field 

studies: Journal of the Water Pollution Control Federation, 

v. 40, no. 2, part 2, p. 285–305.

U.S. Geological Survey, 1981, USGS Quality of Water Branch 

Technical Memorandum No. 81.11; accessed November 6, 

2007, at http://water.usgs.gov/admin/memo/QW/

qw81.11.html

Vomel, H., 2004, Saturation vapor pressure formulations; 

accessed November 6, 2007, at http://cires.colorado.

edu/~voemel/vp.html

Wagner, R.J., Boulger, R.W., Jr., Oblinger, C.J., and Smith, 

B.A., 2006, Guidelines and standard procedures for continuous water-quality monitors: station operation, record 

computation, and data reporting: U.S. Geological Survey 

Techniques and Methods Report 1-D3, 51 p. + 8 attachments; accessed May 22, 2006, at http://pubs.usgs.gov/

tm/2005/tm1D3/pdf/TM1D3.pdf

Weiss, R.F., 1970, The solubility of nitrogen, oxygen and 

argon in water and seawater: Deep-Sea Research, v. 17, 

p. 721–735.

Wilcock, R.J., Nagels, J.W., McBride, G.B., and Collier, 

K.J., 1998, Characterisation of lowland streams using a 

single-station diurnal curve analysis model with continuous 

monitoring data for dissolved oxygen and temperature: New 

Zealand Journal of Marine and Freshwater Research, v. 32, 

p. 67–79.

Wilde, F.D., Radtke, D.B., eds., chapter sections variously 

dated, Field measurements: U.S. Geological Survey Techniques of Water-Resources Investigations, book 9, chap. A6, 

accessed November 6, 2007, at http://pubs.water.usgs.gov/

twri9A6/

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