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Global change is dramatically altering flow regimes worldwide. Among the most important consequences are the transition of many permanent waterways to temporary waterways, the increase in duration and frequency of non-flow periods of temporary streams, and the increase in the severity (i.e. irradiance, temperature and humidity) of the non-flow period. Nowadays, there is a lack of knowledge on how changes in duration, frequency and severity of the non-flow period will reflect on biodiversity and biogeochemical changes in temporary streams. We designed a manipulative experiment using artificial streams to evaluate the effects of severity of the non-flow period on stream biofilms. Sixteen artificial streams were assigned to four treatments: continuous flow, continuous intermittency and intermittency with and without rain events. Effects were assessed on selected features of stream biofilm structure (i.e. bacterial density and basal fluorescence) and function (photosynthetic efficiency and enzymatic activities), as well as CO2 emissions and dissolved organic matter quantity and quality from water column and sediments. The occurrence of rain events during the non-flow period enhanced organic carbon processing and CO2 emissions to the atmosphere, reducing the sediment reservoir of exportable organic carbon and therefore reducing the dissolved organic carbon exports from streambeds at flow resumption. Given the ongoing reducing trends in the frequency of rain events in semi-arid and arid regions, we expect temporary streams to process and emit less and to export more carbon to downstream systems.