Analysing long-term changes in phytoplankton abundance and its drivers will help us understand how marine productivity is changing in the Anthropocene. Theory, models, and some satellite datasets suggest a decline in phytoplankton biomass under climate change, most pronounced in tropical regions as stratification increases, and a shift toward smaller phytoplankton and nitrogen-fixing cyanobacteria. We tested these ideas using long-term observations (14-years) from seven Integrated Marine Observing System (IMOS) National Reference Stations that span 30° of latitude in Australia waters. Although the time series is too short to attribute the phytoplankton response to climate change, having multiple stations spanning tropical to temperate systems provides insights based on space-for-time substitution. We found an overall decline in phytoplankton abundance and biovolume across several, but not all, stations. Temperature was a key driver of the community, with samples from warmer waters having fewer large phytoplankton (diatoms and dinoflagellates) and picoeukaryotes, but more cyanobacteria. A deeper chlorophyll maximum layer also had lower phytoplankton abundance, particularly diatoms and dinoflagellates. Overall, many changes in phytoplankton communities were consistent with theory. Our results suggest that climate change is already influencing phytoplankton abundance and composition in Australian waters, which could have profound effects on higher trophic levels.