Understanding temporal trophic interactions in riverine food webs is essential for predicting river ecosystem function and improving management of these ecosystems. Temporal changes in energy flows through riverine food webs are readily assumed but are rarely tested. Temporal variability in food webs from two reaches of a lowland river (Ovens River, south-eastern Australia) with differing levels of floodplain connectivity were examined over 12 months. We investigated how seasonal changes, flow variability and floodplain connectivity influence (i) stable isotope signatures of basal organic carbon sources (terrestrial sources: trees and grasses; aquatic sources: seston, biofilm and filamentous algae) and consumers (macroinvertebrates and fish) and (ii) the relative proportions of organic carbon sources contributing to consumer biomass using mixing models. We hypothesized (i) that during high flows, increased floodplain connectivity would increase the lateral exchange of terrestrial carbon subsidies to main channel consumers and (ii) that during low flow periods, main channel consumers would derive the majority of their carbon from aquatic benthic sources. Results indicated that isotope signatures for basal sources and for most of the consumers varied temporally and spatially. Mixing models indicated that increased floodplain connectivity did not increase terrestrial subsidies to consumers during high flows. Seston was the primary source during high flows whilst terrestrial vegetation increased in importance during low flows. Filamentous algae was also important during low flows for some consumers. These findings indicate that it is essential to include temporal variability in order to understand energy flows in lowland rivers, thus allowing for the dynamic nature of these ecosystems. © 2010 John Wiley Sons, Ltd.