Globally, many large, lowland rivers are regulated due to the construction of stopbanks and flood protection schemes. Many of these changes now govern discharge regimes and lateral floodplain interactions. These modifications, along with others, contribute to declines in many native fish, including larval Galaxiidae of whitebait. Many attempts to enhance whitebait fisheries within New Zealand have focused on restoring spawning habitat. However, no research has been aimed at understanding the dietary requirements of riverine whitebait and where they source their food from during upstream migration. Previous work has hypothesised that receding floods may introduce large-bodied zooplankton, to the river which may be important for whitebait during upstream migration. The objectives of this research were to investigate (i) the potential of zooplankton to emerge from floodplain soils following inundation, and (ii) whether certain zooplankton groups, indicative of those originating from floodplains, could be a food supply for migrating juvenile Galaxias maculatus in the lower Waikato River. Previous work investigating zooplankton communities in the lower Waikato River floodplain was undertaken during inundation events, but, the origin of zooplankton could not be pin pointed. To test whether inundated floodplain areas developed zooplankton from dormant states in soils, dry soil cores were collected from native forest, scrub (predominantly Salix sp.) and pasture vegetation types, inside and outside of stopbanks to provide different levels of connectivity. Zooplankton emerged from submerged soil within three days of wetting and after 12 days of inundation no new taxa arose. Community composition differed between vegetation types, with larger-bodied cladocerans and copepods dominating native forested and scrub sites, and rotifers dominating pastoral sites. Connectivity did not play a statistically significant role in determining composition of zooplankton communities. Differences in zooplankton composition between sites indicate that floodplain vegetation structure has a dominant role in the development of communities of zooplankton during flooding. Differences in vegetation types were largely due to varying levels of soil moisture, canopy cover and other environmental factors. Gut analyses indicated that juvenile G. maculatus feed on a wide range of aquatic and semi-aquatic organisms. Large-bodied zooplankton and insects found in the gut likely came from multiple sources. Insect presence varied over time whereas Cladocera dominance appeared to be related to flow pulses. Field diet analyses and laboratory selectivity experiments yielded similar results regarding selectivity. Feeding in the laboratory was density-dependent as more food items were consumed at lower fish densities, with no evidence of prey switching to less desirable groups at high densities. This study has increased the understanding of potential food-web linkages between rivers and their floodplains for migrating whitebait populations. The findings of this research indicate that scrub and forested floodplains are important areas for the production and emergence of large-bodied zooplankton following inundation. Transfer of floodplain zooplankton back into the river channel could then be selected by juvenile migrating whitebait as they have shown a feeding preference for large-bodied zooplankton. As a result, management plans have the potential to be implemented to sustain food supplies for migrating whitebait species within large lowland riverine-floodplain environments.