This study analyzed metagenomes of water samples collected from two environmentally distinct locations along the Indian River Lagoon (IRL), a large estuary in eastern Florida where outbreaks of V. vulnificus frequently occur. The metagenomes, obtained from specimens retained on 0.2 micron filters after filtration, were correlated with abiotic and biotic parameters from the two sites, Fellers House and Shepard Park, along the IRL.