This study was conducted to act as a first assessment of the prokaryotic communities of the sediment of the Indian River Lagoon, FL, USA an Estuary of National Significance. The sequences were created using 16S amplicon sequencing on a MiSeq at Research and Testing (Lubbock, TX) using the Earth Microbiome Project modified 515f and 806r primers. It is a two-year survey of 15-19 sites along a 100-mile stretch of the lagoon with the samples taken during four sampling periods about six months apart. The primary goal of this study was to provide a first look at the prokaryotic communities of this important estuary and to assess the impact of freshwater discharges, total organic matter, and copper contamination of sediment microbiomes.