Phytoplankton abundance and taxonomic identification, with emphasis on nanoflagellates was assessed, in the Patos Lagoon estuary and coastal shelf zone. From October 1998 to May 2000 samples were analised through abiotic and biotic (chlorophyll, cell number and taxonomic composition) variables. Microplankton density and identification were determined with an inverted light microscope, and nanoflagellates and picoplanktonic cyanobacteria by epifluorescence. Nanoflagellate’s species composition was determined with transmission electronic microscopy. Richness, genera diversity, and cluster analyzes were analysed to identify spatial, seasonal and salinity classes variations. An increase in chlorophyll-a concentration was detected from the inner Lagoa station to the southern part of the estuary. In 1999 the chlorophyll-a presented a pattern of minimum concentration at the transition zone between the lagoon and the estuary, attributed to salinity increase and high concentration of suspended material, probably more pronounced in La Niña years, as observed in this study when freshwater runoff was low and saline water intrusion reaches the inner transition zone. Relationship between chlorophyll-a and salinity resulted in two groups: lower salinity and chlorophyll-a (Salinity < 10 and < 5g L-1), and with higher salinity and chlorophyll concentration (Salinity > 20 and 0,1- 12 g L-1). Two different microplanktonic groups were identified, one with oligohaline and benthic species (M. dubia, Diploneis, Entomoneis and Surirella), and the other with marine eurihaline species (C. closterium, P. calcar avis, L.minimus). Diversity increased to the southern estuary and coastal zone, in mixomesohaline and mixopolihaline waters. Diversity index in the estuarine region were sometimes high (1-3 bites/ individual) and close to the values usually observed in coastal zones. The low diversity index in the continental shelf (summer 2000) reflects the high density of Pseudo- nitzschia spp. and E. huxley, the only well defined group in cluster analysis. Nanoflagellates density was higher in the southern estuary and continental shelf. The lower salinity group include heterotrophic Paraphysomonas and P. reticulata. The second group with a higher number of species in mesopolihaline and polihaline waters, has approximately 60 species of Chrysochromulina, and Chrysochromulina simplex as the most common. Choanoflagellates constituted the main heterotrophic group, with 16 species and a new one (Diplotheca sp.). Picoplanktonic cyanobacteria cell density (up to 108 cells L-1) was higher in the spring, and forms with phycoerythrin and phycocyanin were positively and negatively related with salinity, respectively, suggesting the existence of different strains or species. In general, nitrogen was the main limiting nutrient controlling primary producers at the estuary, but in several situations absolute and relative silicate concentrations were below the minimum for phytoplankton growth. The N:Si ratio generally lower than 1, suggesting nitrogen limitation, although maximum and medium values were still high. Silicate concentration probably limited diatoms growth in 18% of the samples, more frequently in the southern estuary. This study compared with others in the same área, shows a nitrogen increase in relation to silica (1998- 2000), which was also the driest period, leading to the conclusion that nutrient unbalance resulting from human enrichment sources is manifested in a stronger way in the Patos Lagoon estuary during reduced freshwater runoff, like in La Niña years.