Live benthic foraminifera assemblages were studied in 40 surface sediment samples collected in the Ubatuba Bay (northern coast of São Paulo State) in order to investigate the relationship between the geological, physicochemical parameters and the ecological data. The area has significant contributions of terrestrial inputs from four rivers that flow into the bay. Biological data were analyzed with multivariate techniques of cluster analysis and a Principal Component Analysis (PCA) was carried out for abiotic factors. The Suborder Rotaliina was dominant in the whole studied area. The result of the cluster analysis allowed us to recognize three groups of stations corresponding to three foraminifera assemblages and different environment conditions. The PCA revealed approximately the same three groups obtained with the cluster analysis. A slight increase in diversity in the outer bay was measured. The inner environment is dominated by A. tepida, evidencing local instabilities. Infaunal species are distributed in the middle region associated with mud and a high content of organic matter, while the most external region has similar percentages of epifaunal and infaunal, which indicates the higher energy condition in this portion of the bay. We also quantified the abnormal specimens that were mainly present in the inner bay, especially represented by A. tepida specimens.