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Algal production in rivers fuels foodwebs, and factors controlling this production ultimately affect food availability. Conversely, excessive algal production can have negative effects on higher trophic levels. The present study examined permanent waterholes in a disconnected wet-dry tropical river to determine the controls on algal production. Primary production in this river system was high compared with arid-zone and perennially flowing tropical rivers. Phytoplankton biomass increased over the dry season but this appeared to be because waterhole volume decreased, due to evaporation. Nitrogen (N) was the key limiting nutrient for phytoplankton, with rapid N turnover times, depletion of particulate N-15-nitrogen reflecting increasing N fixationover the dry season, and N stimulation in phytoplankton bioassays. The waterholes were shallow, providing sufficient light for accumulation of benthic algal biomass. Exclosure experiments were also conducted to determine the impact of top-down control on benthic algal biomass, with no evidence that exclusion of fish and crustaceans increased benthic algal biomass. The shallow off-channel waterhole in our study had substantially higher concentrations of nutrients and chlorophyll a than did the on-channel waterholes. This suggests that future anthropogenic changes, such as increased water extraction and increased nutrient inputs, could make the waterholes more vulnerable to deteriorating water quality, such as e. g. algal blooms, low concentrations of dissolved oxygen.