Climate change represents an emerging problem for temporary waters by increasing the frequency and duration of drought periods, with potentially important effects on fluvial biogeochemical processes. Although benthic microbial processes have been recognized to have a most important role in carbon, nutrient and energy flux, few studies have documented the response to dry–wet cycles in temporary waters. Data so far obtained demonstrate that microbial communities are significantly affected by water stress conditions and that their structure changes with a drastic reduction of cell abundance, vitality and metabolic activity. But hydrolytic enzymes constitute an exception to this trend. They are preserved even if the cells in which they originated become non-viable. We postulate that the preservation of these enzymes represents an important mechanism for the fast recovery of surviving microbial cells after flooding and the re-establishment of the metabolic functions of microbial communities.