This study analyzed the temporal variability of phytoplankton assemblages in the surface waters of Guanabara Bay (RJ, Brazil), at six stations in front of Icaraí Inlet from April/2011 to April/2012. Our results highlight the great contribution of diatoms, dinoflagellates and cyanobacteria, represented by 111 taxa typical of estuarine and coastal areas. The coexistence of benthic and planktonic species suggests considerable hydrodinamism in these waters. All variables were homogeneous (p > 0.05) between the stations, but differed between sampling periods. On average, phytoplankton abundance (107 cells.L-1) was higher than that of other estuaries and its temporal behavior was closely correlated (p < 0.01) with diatoms and cyanobacteria. The richness distribution pattern (7 to 27 taxa) was closely correlated (p < 0.01) with dinoflagellates and diatoms. Ninety per cent of all samples presented a low diversity index (< 2.0 bits.cell-1), which indicated the unstable balance of the system, typical of environments subjected to eutrophication. The population structure analysis revealed that 10% of all taxa were resident, 12% visitors and 78% accidental, suggesting the influence of continental and oceanic water influxes. Between the "typical" taxa, the most common were the cyanobacteria of the order Oscillatoriales, the diatoms Ceratoneis closterium (=Cylindrotheca closterium) and Leptocylindrus minimus and the dinoflagellate Prorocentrum triestinum.