The roles of "top-down" and "bottom-up" factors were investigated in terms of their influence on the diatom and dinoflagellate abundances in the microtidal, salt wedge Huon Estuary, Tasmania, Australia. Long-term (1996-2005) changes in Chl a, the peridinin:Chl a ratio and the abundance of autotrophic dinoflagellates were observed to coincide with the warming of regional surface waters. There were significant seasonal differences in pigment-specific net growth rates for Chl a, peridinin and fucoxanthin. Diatoms dominated the spring bloom when species such as Skeletonema costatum had the highest net growth rates and fucoxanthin-specific gross growth rates were ∼0.9 day-1. During late summer, the peridinin-specific grazing mortality was significantly less than the fucoxanthin-specific grazing mortality and dinoflagellates increased their dominance of the phytoplankton community. This late summer relaxation of grazing pressure on dinoflagellates was associated with a decline in the overall abundance of microheterotroph (MH) grazers and a peak in the abundance, biomass and estimated grazing rates of mesozooplankton. We suggest the composition of the autumn phytoplankton community was dependent upon a trophic cascade where mesozooplankton, such as Noctiluca scintillans, preyed upon MHs and reduced their grazing upon some species of dinoflagellates.