The flow regimes in Australia's semi-arid and lowland river systems are among the most variable in the world. The extreme variability of flows in rivers cause “boom and bust” conditions for river food web. High flows may increase turbidity and restrict light availability in the water column and the benthic surface of a river, potentially suppressing autotrophic production. Conversely, high flows can inundate floodplains, where shallow water and high nutrient availability can promote algal productivity. These processes may alter energy availability for primary consumers such as zooplankton, which are a key group of microorganisms that transfer energy through river food webs to higher consumers. We sought to isolate how primary productivity affects zooplankton responses using an outdoor mesocosm experiment. Light availability was reduced in four 2000L recirculating river flumes by shading, and zooplankton responses were compared to four unshaded flumes over six weeks. We found that light climate altered primary productivity, which affected zooplankton abundance and community assemblage. Our results suggest that variability in food source availability is an important mechanism through which changes in river flow can affect river food webs.