Climate change has shifted many smaller headwater streams from a perennial flow regime to an intermittent one during the past decades, potentially affecting their self-purifying capacity. In order to understand the potential changes following the expected higher frequency of droughts in the future, we set up a modelling framework that combines data from field measurements and laboratory studies to make an estimation at the reach scale. Sediment samples taken at different intermittent streams in Austria were analyzed in the lab regarding microbial activity and gas emissions. The field samples were analyzed in different drying stages, and oven-dried to a very low moisture content. Microbial activities were found to be mostly uncorrelated with the water content of the sample, except for the very dry stage, for which a statistically significant decrease could be observed. Two-dimensional hydrodynamic models were set up for each of the streams in order to obtain the wetted areas for a number of low-flow discharges. The modelling framework combines the wetted areas at different simulated flow rates with the measured gas emissions as proxy of microbial activity and thus the self-purifying capacity. In the streams investigated, we could indeed identify reduced microbial activity for lower discharges. This effect increased when assuming a reduction of the shading provided by the vegetation cover of the streambed. Our recommendation for river management is therefore to ensure the availability of a vegetation cover for sustaining the self-purifying capacity of intermittent streams under a warming climate in the future.