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Mesoscale eddies drive variability in phytoplankton functional trait composition and primary productivity (PP) relative to adjacent waters. Offshore waters in southeast Australia are subject to substantial mesoscale eddies that form when the East Australian Current (EAC) travels poleward along the coast, forming distinctive habitats in the upper ocean. Eddies provide an important enrichment mechanism in the nitrogen-limited waters of the Tasman Sea, yet there is limited knowledge of PP within cold- and warm-core eddies in the region and how physico-chemical and biological factors affect phytoplankton communities in this variable environment. We addressed the scarcity of observations by quantifying net PP using 13C isotopic enrichment incubations of surface waters over 10 degrees of latitude, comparing phytoplankton species composition in five different environments: a coastal shelf station, an oceanic cold and warm-core eddy, and a coastal dipole. Cold-core (cyclonic) eddies were significantly more productive than their warm-core (anticyclonic) counterparts (∼35 versus 0 mg C m−3 d−1), with centric diatoms the most prominent phytoplankton group, with a relatively high centric:pennate ratio. The diffuse attenuation coefficient, K d (PAR), and silicate were the best overall predictors of phytoplankton composition, explaining 88% of variation based on pigment analysis and size fractionation. Variance in net PP did not correlate significantly with physico-chemical parameters frequently used in PP models (temperature, K d [PAR], Chl a), yet inclusion of size-fractionated Chl a generated substantial improvement in our statistical model (from 36 to 77%). We show that cold-core eddies play a key role in regulating PP in eastern Australian waters and highlight a need for eddy-resolving models to incorporate descriptors of phytoplankton size structure to improve the accuracy of PP forecasts in eddy intensive regions. • Mesoscale eddies modulate primary productivity dynamics along the East Australian coast. • Knowledge of phytoplankton size structure improves prediction of primary productivity. • Phytoplankton community structure can be predicted from light and silicate levels. • Centric diatoms are the most prominent phytoplankton group in East Australian cyclonic eddies. [ABSTRACT FROM AUTHOR]