Previous studies on the relationship between ecosystem productivity, size and food-chain length have been restricted to comparisons between locations. We examined the effect of temporal variability in productivity on trophic structure of a floodplain ecosystem, hypothesising that during the wet-flood pulses, the increased resource availability might lead to higher food-chain lengths. We examined multiple common sampling locations and species during a severe El Niño drought which followed a consecutive series of historically wet La Niña years, comparing trophic position and dietary sources. While carbon stable isotopes showed no significant difference between the two phases, nitrogen stable isotopes indicated that most species were feeding higher in the food chain in the wet phase. The results suggest that oscillations in climate phase-driven changes have effects on food-chain lengths through changes in productivity, without the introduction of new sources of carbon or changes to the composition of higher-order predators.