This study analyzed kinorhynch communities from the southern portion of Mobile Bay and the near shore Alabama continental shelf. A multicorer was used to collect sediment samples from fourteen sites, specifically targeting the flow of freshwater efflux from the Mobile watershed. These sediment samples were analyzed for kinorhynch species, organic matter content, granulometry and trace metals. Kinorhynch specimens were examined via light microscopy and scanning electron microscopy and identified to species level for community analysis. Eleven species of kinorhynchs were recovered from thirteen sites. Four dominant species, Echinoderes augustae, E. bookhouti, E. spinifurca, and Leiocanthus langi were present, in agreement with an earlier survey of Alabama coastal kinorhynchs. Spearman correlations, PCA, and cluster analyses of kinorhynch communities, along with abiotic data, revealed a patchy distribution of kinorhynchs, organic matter and fine sediments in the path of freshwater efflux. Additionally, this study reports four new species records for the northern Gulf of Mexico.