Temporal variability of physicochemical parameters and phytoplankton primary productivity, abundance and composition were investigated at Babitonga Bay, southern Brazil, using a hierarchical sampling design on the scales of months, weeks and days during spring 2012 and summer 2013. Only temperature, respiration rates and concentrations of dissolved oxygen and silicate exhibited significant differences in the greatest timescale (seasons: spring; summer). In contrast, most physicochemical parameters, such as salinity and the concentration of nitrogen compounds, varied mainly among weeks and days. This short-scale variability was similarly observed for the microphytoplankton abundance, ranging from 0.04 to 1.7.106 cells L–1 during a bloom of the diatom Skeletonema costatum. Two major phytoplankton assemblages were associated with high primary production rates: > 30 μm centric diatoms such as Cyclotella spp. and Cymatodiscus sp., in spring; and a summer assemblage dominated by smaller, bloom-forming diatoms (S. costatum and Eucampia cornuta). Primary production ranged from 10.5 to 1793 mg C m–2 d–1 and varied significantly between days and months, being associated with the photosynthetic active radiation level and weather conditions on the sampling day. Abundance of specific plankton taxa appeared controlled by trophic interactions, as revealed for the mixotrophic, toxic dinoflagellate Dinophysis acuminata complex and its prey, the ciliate Mesodinium rubrum.