Estuaries are transitional areas between streams or rivers and the ocean. Estuaries are affected by fluvial factors, such as freshwater and sediment inputs, and marine factors, including tidal influence, waves, and the inflow of salt water. The inherently dynamic nature of estuaries results in extreme changes in hydrographic characteristics, with the distribution of zooplankton being highly influenced. Zooplankton provide a crucial role in the biological communities of big rivers. However, they are extremely sensitive to environmental changes, particularly in estuarine environments. Consequently, this study aimed to examine how changes in physicochemical properties, such as salinity, affect species richness and zooplankton community composition along the Waikato River estuary, fed by New Zealand’s largest river. Eight sites were selected to represent the salinity gradient from the river mouth to a point where salinity was undetectable. Environmental variables, including temperature, dissolved oxygen, pH, salinity, and chlorophyll-a, as well as zooplankton communities, were examined at spring high tide (25 January 2023), spring low tide (8 March 2023) and neap high tide (15 March 2023). A canonical correspondence analysis (CCA) indicated that salinity explained the greatest proportion of variation in zooplankton community composition (26.8%, P=0.002). At the lower extreme of the gradient, zooplankton assemblages of the freshwater sites were dominated by freshwater rotifers such as Lecane luna, Synchaeta oblonga, Brachionus calyciflorus and Filinia novaezealandiae. The zooplankton assemblages of the saltwater sites were dominated by marine copepods, such as Oithona similis, Paracalanus parvus, Microsetella norvegica, and marine cladocerans such as Pleopis polyphemoides. Dissolved oxygen also significantly influenced zooplankton composition, independent of salinity (9.3%, P=0.004). At sites characterised by intermediate salinities in the Waikato River estuary, typical estuarine copepods (e.g., Gladioferens pectinatus) were absent. Sampling was conducted after high precipitation as well as a severe tropical cyclone which caused heavy rainfall and flooding. The strong influence of the tidal and riverine forces caused an unstable habitat for mid-salinity zooplankton communities to survive. It is predicted that with climate change, extreme weather events will likely become more frequent and severe in the future which pose a threat to less tolerant zooplankton species.