Riparian vegetation typically provides substantial allochthonous material to aquatic ecosystems where micro-organisms can play an important role in organic matter degradation which can support consumer biomass. We examined the effects of leaf litter quality (e. g., leaf nutrients, lignin and cellulose content), leaf species mixing, and microbial community diversity on in-stream breakdown rates of litter from dominant riparian trees (Melaleucaargentea, M. leucadendra, and Naucleaorientalis) in both a perennial and intermittent river in Australia's wet-dry tropics. Leaf mass remaining after 82 days of in-stream incubation was negatively correlated (P < 0. 05) with initial leaf N and P content while initial lignin and cellulose content had no statistically significant effect. Breakdown rates of incubated leaves of both Melaleuca and Nauclea were significantly higher in mixed litter bags compared with single species litter bags. Although it was expected that leaf N content would decrease from initial levels during decomposition, we found either similar or slightly higher N content following in-stream incubation suggesting microbial colonisation increased overall N content. Stable isotopes of ?13C and ?15N for the major sources and consumers in both rivers provide evidence that leaf litter was an important macroinvertebrate food source in the perennial river where heavy shading may limit algal production. However, in the intermittent river where riparian cover was low, benthic algae were the major organic carbon source for consumers. Our findings suggest that riparian tree species influence rates of in-stream organic matter processing, microbial community composition, and aquatic food web dynamics in tropical wet-dry streams.