This study investigated kinorhynch communities from Mobile Bay, Alabama across three sampling transects. A multicorer was used to collect sediment samples from fifteen sites along a northwestern transect (sites 0–4), the Mobile Bay ship channel (sites 5–9 and 14), and a northeastern transect (sites 10–13). Each sediment sample was analyzed for kinorhynch community composition, granulometry, organic matter content, and trace metals. Kinorhynchs were identified to species via light microscopy or scanning electron microscopy for community analysis. Two genera and seven species were recovered from thirteen sites. Three abundant species, Echinoderes augustae, Leiocanthus langi, and Echinoderes bookhouti were found, which were known from recent Alabama surveys in the northern Gulf of Mexico. Echinoderes augustae was the dominant taxon, comprising 85% of the animals identified. Spearman correlations, PCA analysis, and abiotic data revealed a sporadic distribution of animals collected from two distinct sediment profiles. The kinorhynch densities correlated positively with fine sediments and select trace metals (which are indicators of freshwater input), but did not correlate with organic matter content or salinity. Additionally, this study reports two new species records for Mobile Bay.