Quantifying ecosystem-level processes that drive community structure and function is key to the development of effective environmental restoration and management programs. To assess the effects of large-scale aquatic vegetation loss on fish and invertebrate communities in Florida estuaries, we quantified and compared the food webs of two adjacent spring-fed rivers that flow into the Gulf of Mexico. We constructed a food web model using field-based estimates of community absolute biomass and trophic interactions of a highly productive vegetated river, and modeled long-term simulations of vascular plant decline coupled with seasonal production of filamentous macroalgae. We then compared ecosystem model predictions to observed community structure of the second river that has undergone extensive vegetative habitat loss, including extirpation of several vascular plant species. Alternative models incorporating bottom-up regulation (decreased primary production resulting from plant loss) versus coupled top-down effects (compensatory predator search efficiency) were ranked by total absolute error of model predictions compared to the empirical community observations. Our best model for predicting community responses to vascular plant loss incorporated coupled effects of decreased primary production (bottom-up), increased prey search efficiency of large-bodied fishes at low vascular plant density (top-down), and decreased prey search efficiency of small-bodied fishes with increased biomass of filamentous macroalgae (bottom-up). The results of this study indicate that the loss of vascular plants from the coastal river ecosystem may alter the food web structure and result in a net decline in the biomass of fishes. These results are highly relevant to ongoing landscape-level restoration programs intended to improve aesthetics and ecosystem function of coastal spring-fed rivers by highlighting how the structure of these communities can be regulated both by resource availability and consumption. Restoration programs will need to acknowledge and incorporate both to be successful.