Seagrass habitats are critical habitat for many fish species and are currently threatened by anthropogenic and natural factors, such as coastal development, pollution, global climate change, and sea level rise. There are few studies that have tracked long- term changes in seagrass habitat and their associated fish communities. This project addressed this need using data collected by the United States Geological Survey (USGS) from two South Florida sites, North Biscayne Bay, FL (NBB) and Port of Miami, FL (POM). The USGS sampling was part of ongoing monitoring projects designed to assist future management decisions that would enhance the protection of these valuable habitats. Data were collected biannually at the conclusion of the dry (April) and wet (September) seasons from 30 cells at each site. In each cell, the data collected included: six replicates for seagrass species and cover, five sweep net collections for fish species and abundance, as well as abiotic variables (water temperature, salinity, turbidity, water depth, and sediment depth). A distinct loss in fish and seagrass species were observed, particularly between the years of 2011-2014. These years coincided with several events including: the Port Miami Deep Dredge (PMDD) project during the years 2013-2015; periods of drought; and major storm events. Changes in fish community structure over this time period were largely driven by loss of species and increased homogenization of fish communities at both locations. More specifically, the NBB community shifted to resemble that of POM by 2014. These changes mirrored the loss of seagrass cover at both locations. Further studies are required to assess the extent to which ongoing dredging activities and other factors might be affecting seagrass cover, which ultimately affect fish communities.