Both aquatic and terrestrial environments go hand in hand with the conversion of inorganic carbon to other organic compounds known as the carbon fixation process. Florida is one of the most vegetated yet lake-rich states in the nation. The inland lakes of Florida provide perfect sites for studying carbon transport and are a major component of the global scale carbon budget. Studying how the terrigenous organic matter in Florida lakes has an effect on the biogeochemical processes and the microbial communities in these lakes will give insight for understanding nutrient cycles on a global scale. We conducted a study that aimed to understand the impact of terrigenous organic matter on lake microbial taxa related to the carbon cycle. Water and sediment samples were collected from six lakes at the Ordway Swisher Biological Station (OSBS) during both dry and wet seasons. Three of the lakes contained inflow from nearby Cypress swamps and three of the lakes were clear with no surface inflow. Microbial diversity and community compositions were determined using 16S rRNA gene-based amplicon sequencing. It was found that organic matter from the forest had an effect on the composition and functions of the microbes in the darker lakes.