SummaryA consequence of drought in streams is the emersion of decomposing leaf litter, which may alter organic matter recycling. We assessed the effects of emersion on decomposition of black poplar leaves and associated microbes (microbial biomass, extracellular enzyme activities and microbial diversity) in two streams with distinct characteristics, in particular nutrients, temperature and oxygen levels. Leaf decomposition rates, fungal biomass and extracellular enzyme activities were lower in the most impacted stream (high nutrients and temperature, low oxygen). Also, the structure of fungal and bacterial communities differed between streams. Emersion strongly affected all microbial functional measures. Leaf decomposition, fungal biomass and extracellular enzyme activities were more sensitive at the most pristine site, while fungal reproduction and bacterial biomass production were more affected by emersion at the most impacted stream. Microbial community structure was strongly altered after emersion. Although similar effects on leaf‐associated microbes were found in both streams, functional responses to emersion differed probably as a consequence of different initial microbial communities with different sensitivity to the drying stress. Our study highlights the need of understanding the effects of drought in streams suffering from different environmental perturbations, since responses to emersion appear to depend on the environmental context.