Studies aimed at determining phytoplankton composition, biomass, ecology and some physical-chemical characteristics of the São Francisco estuary were conducted at 7 sampling stations located in Piaçabuçu-Alagoas (10º25’-10°30’S and 36º23’-36º27W) during the rainy and dry seasons. The samples were obtained from the subsurface layer at neap and spring tides, during high and low tides, using a plankton net with 45 um mesh size. The waters from this estuary are characterized by low salinity, high temperatures, pH between alkaline and slightly acid, transparency greater than 1 meter. The phytoplankton was composed of 205 taxa, mainly distributed between the divisions Chlorophyta and Bacillariophyta, considered the most representative. The diatom Aulacoseira ambigua was considered dominant. Most of the species identified were planktonic and of freshwater origin. Specific diversity and equitability were considered average and high, indicating conditions of environmental equilibrium in the studied area. The analysis of variance in taxonomic richness revealed higher averages for the dry season and for high tides. Chlorophyll a content ranged between 0.4ug/L and 24,4ug/L. The annual variation of phytoplankton and physical-chemical parameters was related to rainfall.