Human activities have greatly altered the flow regime of rivers worldwide. Within the Murray-Darling Basin in Australia, flow regulation has altered natural flows primarily as a consequence of water abstraction for irrigation. These changes are expected to affect zooplankton, a key group of microorganisms that feed on bacteria and algae and are preyed upon by predators such as larval fish. The composition of zooplankton communities is critical to the movement of energy through river food webs to higher consumers. However, it is not well understood how flow magnitude affects hydraulic habitat and what the implications are for zooplankton communities. We sampled zooplankton from littoral, mid-channel, pelagic and submerged log (snags) habitats in the Lachlan River, central NSW, using a battery-powered pump and plankton net. The habitats differed in water velocity, with snag, littoral, and pelagic habitat patches having average velocities of 0.01m s-1, 0.05m s-1, and 0.30 m s-1, respectively. We found that the slow flowing areas in the littoral zone and near submerged logs supported high zooplankton abundance (200 individuals L-1 and 121 individuals L-1 respectively) compared to mid-channel habitats (107 individuals L-1). Rotifers dominated the zooplankton community (97.5% of individuals) followed by the copepods (1.3%) and cladocerans (1.2%). Our results suggest that low flow conditions increase zooplankton abundance and highlight the importance of maintaining and restoring in-channel structures such as large woody debris. Managing water through the delivery of environmental flows to inundate shallow near-channel floodplains may be an optimal strategy to support zooplankton communities and enable efficient energy flow through river food webs.