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Spatial and temporal widening of drought periods together with occurrence of flash storm events are consequences of global change affecting temporary stream ecosystems. Streambed heterotrophic microbes and the key biogeochemical processes they carry on could be endangered by the strengthening of drought episodes. Here, we performed a 165-day experiment through 12 streambed sediment columns to study heterotrophic microbial functional and structural responses to long-term drought. Two sediment depths (surface and hyporheic) and leaf litter were monitored under three treatments: control (maintained in wet, pool-like conditions), dry (5 months of drought), and dry-storm (5 months of drought including two flash storms). All treatments were then followed by rewetting. Surface sediment followed by leaf litter was the most affected by the long-term drought as shown by the reduction of polysaccharidic enzyme activities and litter decomposition rate, although lignin decomposition was not affected. This resulted in a greater use of recalcitrant compounds which might be due to reduced labile organic matter sources and the greater resistance of fungi than bacteria to drought. Moreover, in surface sediment, bacterial viability and algal biomass were reduced while the production of extracellular polymeric substances was intensified with dryness, suggesting its potential role as survival strategy. Hyporheic sediments appeared more resistant to long-term drought, and this might be linked to its slightly higher water content (2.5%) than the surface (0.5%) during drying together with a greater content of fine material that allowed fungi and bacteria to survive and extracellular enzyme activities to be maintained. Microbial resilience to long-term drought in sediment and leaf litter was promoted by the flash storms as shown by the fast recovery of enzyme activities, bacterial viability and leaf litter decomposition rate in the dry-storm treatment, once rewetted. Storms might liberate previously occluded carbon sources that fuel the fast microbial reactivation as well as providing sediment moisture for microbial survival. Our results highlight that long-term drought may compromise stream biogeochemical processes linked to organic matter decomposition and that microbes are highly sensitive to minimal water content changes. Thus, long-term drought consequences could be mitigated by occasional precipitations or by natural streambed moisture.