The Huron River watershed is comprised of three primary land uses: agricultural, natural, and urban. Land usage affects the biological and chemical conditions within the watershed, therefore affecting water quality. Recent studies have provided evidence that water quality can be assessed by examining the composition of the microbial communities found in biofilms. In this study we analyzed and compared samples collected from a natural site and urban site over the course of three seasons; fall (August), winter (December), and spring (April). Microbial diversity was determined by isolating, amplifying, and genotyping the 16S rRNA gene. The results show that microbial community structure varies with seasons, material composition, and site location.