Understanding phytoplankton dynamics is critical across a range of topics, spanning from fisheries management to climate change mitigation. It is particularly interesting in the East Australian Current (EAC) System, as the region’s eddy field strongly conditions nutrient availability and, therefore, phytoplankton growth. Numerical models provide unparalleled insight into these biogeochemical dynamics. Yet, to date, modelling efforts off southeastern Australia have either targeted case studies (small spatial and temporal scales) or encompassed the whole EAC System but focused on climate change effects at the mesoscale (with a spatial resolution of 1/10º). Here we couple a model of the pelagic nitrogen cycle (bio_Fennel) to a 10-year high-resolution (2.5–5 km horizontal) three-dimensional ocean model (ROMS) to resolve both regional and finer scale biogeochemical processes occurring in the EAC System. We use several statistical metrics to compare the simulated surface chlorophyll to an ocean colour dataset (Copernicus-GlobColour) for the 2003–2011 period and show that the model can reproduce the observed phytoplankton surface patterns with a domain-wide rmse of approximately 0.2 mg chla m −3 and a correlation coefficient of 0.76. This coupled configuration will provide a much-needed framework to examine phytoplankton variability in the EAC System providing insight into important ecosystem dynamics such as regional nutrient supply mechanisms and biogeochemical cycling occurring in EAC eddies.