Leaf-litter decomposition in forested streams is a key process that fuels food-webs. However, drivers of this process in intermittent streams are poorly understood. Our goal was to compare the microbial-mediated decomposition of three leaf species [all native in temperate riparian forests from Portugal (alder, chestnut and oak)] in the channel and its riparian zone of an intermittent stream. The leaves were incubated for 88 days, the stream channel presenting a total of 8 days of water flow, 49 days of isolated pools, and 35 days running dry, while the riparian zone remained emerged the whole time. Alder decomposed faster than the other species in both areas which is related to its higher quality. Independently of the species, decomposition rates were higher in the stream channel (1.4- to 1.8-fold) than in the riparian area. Fungal biomass also differed among species, oak having the lowest value. The different quality between alder and chestnut was not translated into differences in fungal biomass, which may be related to an earlier fungal peak and faster decomposition of the former. Between zones, leaves incubated in-channel presented higher fungal biomass than those in the riparian zone, being higher for chestnut (3.8-fold) in comparison with the other species (1.8- fold for alder and 2.0-fold for oak). These results strengthen the key role of water (sensu lato) as a driver of litter decomposition. The synchronous or asynchronous presence of lotic and lentic environments in the streambed, associated with soil humidity in drier periods, seem to enhance fungal growth, accelerating litter degradation in-stream. A delayed terrestrial degradation and the distinct leaf species-specific susceptibility to changes in environmental conditions may constitute an insurance, for the stream communities, of a higher quality of leaf material supplied to the stream by the riparian area when flow resumes.