Changes in epilithic cyanobacterial communities were determined in a river characterized by variations in nutrient content. The cyanobacterial community composition of the upstream sites was different from that of the downstream communities, where anthropogenic influences lead to an increase in nutrients (principally soluble reactive phosphate, SRP). There was a general trend in downstream sites towards a decrease in species richness, abundance, and diversity of cyanobacteria. The reduced cyanobacterial species richness in downstream locations was due largely to a marked decrease in the number of heterocystous species, although the number of non-heterocystous species also decreased. Epilithic phycobiliprotein content was positively correlated with the number of cyanobacterial cells, implying that this pigment provides information about the abundance of the cyanobacteria community in the epilithon. The lowest concentrations of phycobiliprotein in the epilithon were observed where concentrations of phosphate were highest. Similarly, the number of heterocystous and non-heterocystous species tended to decrease as the SRP increased, and as the DIN:SRP ratio decreased. However, no relation was found with dissolved inorganic nitrogen (DIN). The differences among cyanobacterial communities could be interpreted as being a consequence of variations in nutrient composition. Finally, the usefulness of cyanobacteria as an alternative tool for assessing changes in water quality is discussed.