Freshwater inflow events play a major role in structuring estuarine zooplankton communities. Freshwater inflow events affect zooplankton directly through advective forcing and changes in salinity, and indirectly through changes to resources by the delivery of organic carbon and nutrients that can stimulate microbial and primary production. Here, we investigate changes to estuarine zooplankton assemblage structure, density and δ13C stable isotopes during a period of highly variable freshwater inflow in the Bega River estuary, Australia. High inflows resulted in a reduction of salinity and a shift in the zooplankton assemblage structure from purely estuarine taxa towards freshwater taxa. The density of select genera of rotifers, cladocera and, in the upper estuary, copepods, increased following inflows, concurrent with increases in the concentration of dissolved organic carbon and bacterial biomass. Redundancy analysis found that environmental variables including discharge, dissolved organic carbon, salinity and bacterial biomass explained 66-73% of zooplankton variation. Stable isotope results indicated that all copepod and cladocera species tested were predominantly supported by allochthonous carbon from terrestrial sources. The present results have provided important evidence that freshwater inflows play a critical role in structuring zooplankton assemblages and supporting increased production through the delivery of allochthonous organic carbon.