USGS Techniques and Methods 4-C2

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

U.S. Geological Survey Techniques and Methods 4-C2, 33 pages (Published online January 2008)

This report is available in PDF format: TM4-C2 (Opens the PDF file in a new window. ) (16.6 MB)

Cover thumbnailIn 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.




Purpose and Scope

Theoretical Background


Dissolved-Oxygen Saturation Concentration

Correction of Measured Dissolved-Oxygen Concentration for Sensor Error and Drift

Determination of Analysis Period

Reach-Averaged Water Temperature, Dissolved-Oxygen Concentration, and Dissolved-Oxygen Deficit


Net Metabolism


Gross Primary Production and Net Ecosystem Production

User’s Guide

Two-Station Method

Single-Station Method


To view the PDF document, you need the Adobe Reader installed on your computer. (A free copy of the Adobe Reader may be downloaded from Adobe Systems Incorporated.)

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

For more information, please contact Jerad D. Bales.

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