The goal of this study was to assess the epiphytic diatom community structure of two host species along a karst gradient in the upper Green River, Kentucky to a gain a better understanding of the role of diatoms in the food web. The host species studied were Podostemum ceratophyllum and Cladophora. Percent cover of P. ceratophyllum and Cladophora were quantified in the four study reaches. The host species were sampled near-shore and mid-channel in each reach in September and October of 2013. After diatoms were extracted from the host and enumerated the density and diversity were quantified. Twelve genera were identified with > 91% of the community in each reach being Cocconeis. The second most abundant genus was Achnanthes or Navicula depending on the reach. The density and diversity of diatoms increased longitudinally going downstream. Exceptions to this trend occurred when high flow events disturbed the community. Within reaches there were no differences in diatom diversity in near-shore and mid-channel habitats. Diatom density in near-shore and mid-channel habitats was only different in the most downstream reach. Cladophora had a community twice as dense as P. ceratophyllum, but less diverse. The results of this study indicate that there are longitudinal differences in diatom communities in the upper Green River and host species are an important factor in determining the community composition. The importance of epiphytic diatoms in the food web, however, remains unclear.