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Phytoplankton community composition, productivity and biomass characteristics of the mesohaline lower Neuse River estuary were assessed monthly from May 1988 to February 1990. An incubation method which considered water-column mixing and variable light exposure was used to determine phytoplankton primary productivity. The summer productivity peaks in this shallow estuary were stimulated by increases in irradiance and temperature. However, dissolved inorganic nitrogen loading was the major factor controlling ultimate yearly production. Dynamic, unpredictable rainfall events determined magnitudes of seasonal production pulses through nitrogen loading, and helped determine phytoplankton species composition. Dinoflagellates occasionally bloomed but were otherwise present in moderate numbers; rainfall events produced large pulses of cryptomonads, and dry seasons and subsequent higher salinity led to dominance by small centric diatoms. Daily production was strongly correlated (r = 0·82) with nitrate concentration and inversely correlated (r = −0·73) with salinity, while nitrate and salinity were inversely correlated (r = −0·71), emphasizing the importance of freshwater input as a nutrient-loading source to the lower estuary. During 1989 mean daily areal phytoplankton production was 938 mgC m−2, mean chlorophyll a was 11·8 mg m−3, and mean phytoplankton density was 1·56 × 103 cells ml−1. Estimated 1989 annual areal phytoplankton production for the lower estuary was 343 gC m−2.