Vegetated coastal seascapes exhibit dynamic spatial patterning, some of which is directly linked to human coastal activities. Human activities (e.g. coastal development) have modified freshwater flow to marine environments, resulting in significant changes to submerged aquatic vegetation (SAV) communities. Yet, very little is known about the spatially complex process of SAV habitat loss and fragmentation that affects ecosystem function. Using habitat mapping from aerial photography spanning 71 years (1938-2009) for Biscayne Bay (Florida, USA), we quantify both SAV habitat loss and fragmentation using a novel fragmentation index. To understand the influence of water management practices on SAV seascapes, habitat loss and fragmentation were compared between nearshore and offshore locations, as well as locations adjacent to and distant from canals that transport freshwater into the marine environment. Habitat loss and fragmentation were significantly higher along the shoreline compared with offshore seascapes. Nearshore habitats experienced a net loss of 3.31% of the total SAV mapped (2.57 km2) over the time series. While areas adjacent to canals had significantly higher SAV cover, they still experienced wide fluctuations in cover and fragmentation over time. All sites exhibited higher fragmentation in 2009 compared with 1938, with four sites exhibiting high fragmentation levels between the 1990s and 2000s. We demonstrate that freshwater inputs into coastal bays modify the amount of SAV and the fragmentation dynamics of SAV habitats. Spatial changes are greater close to shore and canals, indicating that these coastal developments have transformative impacts on vegetated habitats, with undetermined consequences for the provisioning of ecosystem goods and services.