1.The estimation of stream metabolism represents a useful technique for characterizing the ecological status of natural lotic systems. The existing tools for investigating metabolism in situ demand expert knowledge, provide only a few options, ignore possible groundwater effects and often rely on modeled input data, such as gas exchange, that could be subject to error.

2.We have developed MeCa, a user-friendly MATLAB toolbox that contains different options – including the groundwater correction - for the calculation of metabolism. A detailed explanation of all the calculation steps and the various calculation options is given in the appendix. The functions of MeCa can be tested using the test dataset provided.

3.We conducted sensitivity tests to assess the effect of certain parameters (reaeration, travel time, groundwater oxygen concentration, mean depth and width) and other measurements (oxygen, temperature, pressure) on the metabolism estimation. Uncertainties in the parameters have a greater effect than those that apply to the measurements. The parameters reaeration coefficient and mean depth are the most sensitive input data.

4.Results from sensitivity analyses show the complexity of metabolism studies in streams and the importance of direct calculations. MeCa includes all relevant calculation options, and thus makes a contribution towards the standardization of metabolism studies.