Climate change models for Central Europe predict frequent occurrence of drought and fragmentation of low order streams into a series of pools in summer and autumn. We tested the effect of such drought on litter decomposition processes and dynamics in a lowland stream currently shifting from permanent to intermittent flow regime. We monitored litter input, water level, stream temperature, and oxygen concentration. We assessed leaf associated microbial and macroinvertebrate colonization and activity, and litter decay rates during and after the fragmentation period. The drought event caused stream fragmentation and premature litter input. During fragmentation stream temperature and oxygen concentration were low and controlled by seepage of shallow groundwater. Litter decay in pools was slow and predominantly microbial mediated. Press disturbance, such as low oxygen and/or predation caused low diversities and low abundances of macroinvertebrates and aquatic hyphomycetes. As fragmentation persisted until mid-winter, the litter accumulated on the stream bottom. After stream fragmentation, decay of the accumulated litter was slow, due to low winter-temperatures and slow re-colonization of macroinvertebrate shredders. Our results reveal that drought events can desynchronise the litter input and decay processes and may have long term repercussions for the stream organic matter budget.