Rodrigo de Freitas Lagoon is an urban ecosystem undergoing accelerated degradation, therefore selected as a model for microbiological quality studies of tropical lagoons. The aim of this study was to evaluate the abundance and the spatial distribution of fecal pollution indicators and pathogenic microorganisms in the lagoon. The relationships between microbial groups and abiotic measurements were also determined to evaluate the influence of environmental conditions on bacterial distribution and to identify the capability of coliforms and Enterococcus to predict the occurrence of Vibrio, Staphylococcus aureus, and Salmonella. Surface water samples were collected monthly, from December 1999 to October 2000. Analyses were performed by traditional culture techniques. A uniform spatial distribution was observed for all bacterial groups. The fecal pollution indicators occurred in low abundances while potentially pathogenic microorganisms were consistently found. Therefore, our study supported the use of counts of coliforms and Enterococcus to indicate only recent fecal contamination.