In Australia's Wet Tropics rivers, perennial base flows punctuated by wet season floods drive instream responses across a range of spatial and temporal scales. We combined gut-content and stable-isotope analyses to produce preliminary webs depicting trophic links between fish, their main prey items and basal productivity sources. We then used these webs to test the applicability of general food web principles developed in other tropical systems. Although a range of sources appeared to underpin fish productivity, a large portion of total energy transfer occurred through a subset of trophic links. Variability in food web structure was negatively correlated with spatial scale, being seasonally stable at river reaches and variable at smaller scales. Wet Tropics rivers are similar to those in other tropical areas, but exhibit some unique characteristics. Their high degree of channel incision improves longitudinal connectivity, thereby allowing fish to move between mesohabitats and target their preferred prey items, rather than shifting their diet as resources fluctuate. However, this also inhibits lateral connectivity and limits terrestrial energy inputs from beyond the littoral zone.