In 2019, an unusual mortality event (UME) occurred in common bottlenose dolphins (Tursiops truncatus) in the Mississippi Sound due to exposure to prolonged low salinity. Lesioned and non-lesioned skin samples from four dolphins that died during this UME were collected to characterize the microbiome and potentially determine associations of bacterial types with freshwater lesions. For comparison, microbiome analysis was also conducted on skin samples from two other stranded dolphins from the Mississippi Sound (not associated with the 2019 UME). 16S metagenomic libraries were prepared from nine skin samples, and the V3 and V4 variable regions were amplified and sequenced. Clustering of the sequence reads produced 1,043 operational taxonomic units (OTUs) at the genus level from the nine samples. Based on normalized read counts, the genera Asinibacterium, Alistepes, and Barnesiella had significantly increased abundance in skin samples from dolphins with freshwater lesions compared to dolphins without lesions. Other genera that had large fold increased abundance in dolphins with freshwater lesions included Aeromomas, Arcobacter, Bacteroides, Flavobacterium, and Vitreoscilla. Intersection analysis showed that paired samples from the same dolphin (lesion versus non-lesion skin samples) shared a large number of common OTUs. The seven samples from dolphins with freshwater lesions also shared a large number of common OTUs, as did the two samples from dolphins without skin lesions. These results indicate that lesioned skin and non-lesioned skin samples from the same dolphin shared more similarity than lesioned samples from different dolphins. Furthermore, the seven samples from dolphins with freshwater lesions were similar to each other, as were the two samples from dolphins with non-lesioned skin. In summary, dolphins have variation in their individual skin microbiomes, but their skin microbiomes have similar changes following prolonged freshwater exposure.