This study was conducted, in collaboration with industrial stakeholders, to determine how the health, fatty acid profiles, microbiome, and transcriptome of Florida pompano larvae change in response to being raised at different salinities. Water samples were taken every six days for microbiome analysis while tissue (DNA and RNA) and biochemical samples every three days. Extracted DNA samples were sent to GeneWiz (South Plainfield, NJ, USA) for 16S EZ sequencing to amplify the bacterial/archaeal 16S V3V4 region using the proprietary primers. Larvae were grown at three salinities in triplicate over a period of 24 days post hatching. The primary goal of this study was to determine if the larvae could survive at lower salinities, saving costs associated with farmers maintaining a higher salinity.