Zooplankton are sensitive indicators of climate variability and environmental change, providing insights into ecosystem health and food for higher trophic levels. We use the largest zooplankton dataset in Australia, from the Integrated Marine Observing System (IMOS), to investigate temporal and spatial variation, and their drivers, from seven sites around Australia. We found that biomass varied annually, and seasonally at most sites. Seasonal patterns were observed in biomass of temperate sites in Maria Island (TAS) and Port Hacking (NSW), where such variation is expected, but seasonality was also observed in tropical Yongala in North Queensland. Sea Surface Temperature (SST) was the main driver of each location’s distinct copepod communities, with El-Nino Southern Oscillation signals being felt in communities at monitoring stations based in Port Hacking, and Maria and Rottnest Island. Warm-water communities were dominated by smaller species like Parvocalanus crassirostris, and temperate communities had a higher composition of larger species like Calanus australis. We conclude that many hypotheses commonly used conceptually in zooplankton ecology often hold broadly, but are only sometimes applicable at the local scale. Future increases in ocean temperatures are likely to have an impact on copepod communities, with expansion of warm-water communities poleward ultimately affecting fisheries and ecosystems.