The density of Bifidobacterium spp., fecal coliforms, Escherichia coli, and total anaerobic bacteria, acridine orange direct counts, percentages of total bacterial community activity and respiration, and 12 physical and chemical parameters were measured simultaneously at six sites for 12 months in the Mameyes River rain forest watershed, Puerto Rico. The densities of all bacteria were higher than those reported for uncontaminated temperate rivers, even though other water quality parameters would indicate that all uncontaminated sites were oligotrophic. The highest densities for all indicator bacteria were at the site receiving sewage effluent; however, the highest elevation site in the watershed had the next highest densities. Correlations between bacterial densities, nitrates, temperature, phosphates, and total phosphorus indicated that all viable counts were related to nutrient levels, regardless of the site sampled. In situ diffusion chamber studies at two different sites indicated that E. coli could survive, remain physiologically active, and regrow at rates that were dependent on nutrient levels of the ambient waters. Bifidobacterium adolescentis did not survive at either site but did show different rates of decline and physiological activity at the two sites. Bifidobacteria show promise as a better indicator of recent fecal contamination in tropical freshwaters than E. coli or fecal coliforms; however, the YN-6 medium did not prove to be effective for enumeration of bifidobacteria. The coliform maximum contaminant levels for assessing water usability for drinking and recreation appear to be unworkable in tropical freshwaters.