1. The effects of flooding on top predators are poorly understood globally, but particularly in monsoonal streams. We therefore attempted to assess how inter-annual and intra-annual variations in flood magnitude affected an obligate riverine predator, the brown dipper (Cinclus pallasii), and its invertebrate prey, in the mountain Tachia River, Taiwan. Major flooding in one of the study years (2005) allowed an insight into the effects of abnormally large flows. 2. The abundance and biomass of insects, and the abundance of dippers, decreased steadily from 2003 to 2005 as flood magnitude grew, but then increased in 2006 when more typical discharge returned. Dipper abundance, insect abundance and insect biomass were all strongly positively inter-related, but negatively related to discharge. Insect biomass, rather than abundance, was more useful in predicting brown dipper abundance. 3. Aquatic insect composition fluctuated among sampling years, revealed by non-metric multidimensional scaling, and these fluctuations were also related to discharge. In turn, dipper abundance and the mean body size of aquatic insects declined with the shift in insect composition as flow increased. 4. These data illustrate how discharge fluctuations can have pronounced effects on top predators in streams, mediated in this case by fluctuating prey abundance. While contributions from bird movement, breeding performance and mortality were not clearly differentiated, our data reveal how dippers have strategies to accommodate varying discharge in river systems. We suggest that the effects of floods on dippers should be taken into account when using this group as indicators of river quality