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Dryland rivers are characterised by highly pulsed and unpredictable flow, and support a diverse biota. The present study examined the contribution of floodplain sources to the productivity of a disconnected dryland river; that is a waterhole, after a major overland flood event. Rate measures of productivity were combined with stable isotope and biomass data on the food web in the waterhole and floodplain. The present study estimated that 50% of the fish carbon in the waterhole after flooding was derived from floodplain food sources. In the few months after retraction of the river to isolated waterholes, the large biomass of fish concentrated from the flooding decreased by 80%, most likely as a result of starvation. Based on the development of a carbon budget for the waterhole, mass mortality is hypothesised to be the cause of the high rates of heterotrophic production in the waterhole. The present study suggests that floodplain inputs are important for fuelling short-term production in waterholes, but via an unconventional pathway; that is, fish mortality. The episodic nature of flooding in dryland rivers means that changes in flow regimes, such as water regulation or abstraction, will reduce flooding and hence floodplain subsidies to the river. This is likely to have significant impacts on river productivity.