Submerged aquatic vegetation (SAV) communities display complex patch dynamics at seascape scales that are presently poorly understood as most studies of disturbance on SAV habitats have focused on changes in biomass at small, quadrat-level scales. In this study, analyses of remote sensing imagery and population modelling were applied to understand SAV patch dynamics and forecast the fate of these important communities in Biscayne Bay, Miami, Florida, US. We evaluated how the proximity of freshwater canals influences seagrass-dominated SAV patch dynamics and, in turn, how patch-size structure influences the stability of seagrass seascapes under different salinity scenarios. Seagrass fragmentation rates were higher in sites adjacent to freshwater canals compared to sites distant from the influences of freshwater deliveries. Furthermore, we documented a clear trend in patch mortality rates with respect to patch size, with the smallest patches (50 m2) undergoing 57% annual mortality on average. The combination of higher fragmentation rates and the higher mortality of smaller seagrass patches in habitats exposed to pulses of low salinity raises concern for the long-term persistence of seagrass meadows in nearshore urban habitats of Biscayne Bay that are presently targets of Everglades restoration. Our model scenarios that simulated high fragmentation rates resulted in SAV population collapses, regardless of SAV recruitment rates. The combined remote sensing and population modelling approach used here provides evaluation and predictive tools that can be used by managers to track seagrass status and stress-response at seascape levels not available previously for the seagrasses of South Florida.