To examine temporal changes in a bacterial community, water samples were collected monthly for one year from five sites along a major use-reuse river, the Cuyahoga River, in northeastern Ohio (USA). Fluorescent in situ hybridization (FISH) was used to enumerate population sizes of two species of common bacteria, Pseudomonas putida and Acinetobacter calcoaceticus; FISH was also performed with a Domain Bacteria specific probe. In addition, the total bacteria (based on DAPI staining), colony forming units (on modified Nutrient agar) and coliforms were enumerated and supporting physical/chemical data were collected. Each variable examined exhibited a different seasonal pattern. Temporal changes in total number of bacteria and population size of P. putida were correlated with turbidity and precipitation suggesting that allochthonous sources and scouring of the benthos may be major contributors to these portions of the community. In contrast, the number of cells hybridizing the Domain Bacteria and A. calcoaceticus probes were correlated with temperature. Thus, different aspects of the bacterial community are potentially controlled by different factors and the role of allochthonous and autochthonous sources may vary among species.