Flood events can play a critical role in mobilising nutrients and allochthonous energy for riverine food webs. This influx of allochthonous carbon and nutrients may have significant effects on the aquatic food web by influencing the microbial loop and metazoan communities. In highly regulated rivers where these natural flood events are greatly reduced, environmental flows may be used in an attempt to increase floodplain inundation and allochthonous input. This study focuses on the highly regulated Namoi River in central eastern Australia to understand how bacteria, phytoplankton and zooplankton respond to high flow events that cause floodplain inundation and how this may be affecting native fish communities. After a large flood event which inundated surrounding floodplains zooplankton communities shifted with rotifer communities changing and abundance decreasing while copepod and cladoceran abundance increased. Increases in DOC concentrations and turbidity were observed as well as a general decrease in phytoplankton concentrations. This suggests maintaining connectivity to the floodplain is important for metazoan production and allochthonous input can subsidise food webs in times of low primary production.