The spatial and temporal patterns of environmental heterogeneity in a Brazilian coastal lagoon were described by means of principal component analysis. Carapebus Lagoon has been subject to eutrophication, due to increased nutrient loading from domestic and industrial sewage. Spatial variations in the trophic state and temporal variations in the degree of marine influence are the major sources of environmental heterogeneity in this lagoon. The close and significant relation between total phosphorus and chlorophyll a (r(2) = 60, p<0.05), and the high TN:TP ratios (up to 50:1) suggest that phosphorus might be the major nutrient controlling phytoplankton biomass in this lagoon. However, nitrogen might be more important as a growth-limiting nutrient in the eutrophic site of the lagoon, where high total phosphorus concentration (up to 338 mu g l(-1)) and low TN:TP mass ratios (<10:1) were found. In a multiple regression model, total phosphorus and electric conductivity explained together a high and significant (R-2=0.86, p < 0.001) amount of variance in chlorophyll yields. This predictive model of chlorophyll a is important as a tool for Carapebus lagoon management because it allows one to predict the algal biomass development of the lagoon in response to nutrients and marine water inputs resulting from man's activities.