Fish larvae require high densities of appropriately sized prey items for their survival and recruitment. It has been widely assumed that inundated floodplains are the major source of high densities of prey in floodplain rivers. This study examined the density and distribution of both pelagic and epibenthic meiofauna in a range of potential larval fish nursery habitats within the main channel of an Australian floodplain river. Although sufficient densities of meiofauna were found in the main channel environment to sustain fish larvae, the prey source was predominantly in the epibenthic zone, where the density of meiofauna was on average 100 times greater than in the pelagic zone. There was no apparent relationship between the density of meiofauna, both epibenthic and/or pelagic, and the preferred nursery habitats of fish larvae. This study suggests that an abundant prey resource for developing fish larvae may exist in main channel environments without inputs from the inundated floodplain. However, further studies are required to determine the relative contributions and importance of prey resources on inundated floodplains compared to the main channel environment for larval survival and cohort strength between successive years. Additionally, this study highlights the importance of sampling the epibenthos, and suggests that the significance of epibenthic meiofauna has been severely underestimated in many previous studies.