Microbial diversity and function in intermittent rivers and ephemeral streams (IRES) are tightly linked to specific habitat availability and hydrological phases. The intensity and frequency of the different phases (especially drying and rewetting) affect community composition and key functions, mainly linked to biogeochemical processes. Resistance and resilience strategies are distinct among microorganism groups-bacteria, archaea, fungi, protozoans-and strongly depend on different types of microhabitat or refuge available. The biodiversity of prokaryotes in IRES is strongly affected by hydrology but microhabitat conditions and type of benthic substrate significantly affect their community composition. Fungi are very sensitive to drying but use several refuges, including the terrestrial habitat, and resistance strategies. Protozoans show a wide range of survival strategies and several species can resist harsh conditions such as anoxia in drying pools. Thus, they become especially relevant for ecosystem functions when other organisms are inhibited. This sensitivity causes "waves" of microbial functions and biodiversity to covary with hydrological phases, potentially affecting ecosystem functioning and higher trophic levels. Microbially mediated functions in IRES are perhaps the most critical to freshwater ecosystem services such as nitrogen and carbon cycling. Therefore, efforts to manage and restore IRES will depend on improved understanding of hydrological controls on microbial communities and functions across space and time.