Flow pulses that alternately immerse and expose benthic habitats are widely recognized as key determinants of biodiversity and ecosystem functioning in rivers. Terrestrial leaf litter input, colonization, and breakdown are also key processes in river ecosystems, but little is known about the effects of alternating immersion and emersion on these processes. We used litterbags to examine breakdown, microbial activity, and colonization of Populus sp. leaves by invertebrates along a natural gradient in immersion and emersion (i.e., submergence and exposure to air) in a temporary river. Rates of leaf litter mass loss, microbial activity and colonization by invertebrates differed among litterbags that were permanently immersed, intermittently immersed and permanently emersed, and breakdown rate coefficients (k) decreased with increasing cumulative emersed duration (the total number of day of emersion during the experiment). In contrast, the frequency of emersed periods had no detectable effects on these variables. k was positively correlated with the density of invertebrate shredders in immersed litterbags, with microbial activity and shredder density in intermittent litterbags, and with microbial activity in emersed litterbags. These correlations suggest that the relative importance of microbial activity on k increases with emersed duration, due to the periodic elimination of aquatic shredders and the scarcity of terrestrial detritivores. The fact that leaf litter breakdown was detectable under permanently emersed conditions indicates that mechanisms other than shredding by invertebrates, such as leaching and photodegradation, are dominant in dry river habitats.