A central challenge for water managers is to adaptively manage water availability to meet societal needs while simultaneously protecting ecosystems. Progress restoring the Everglades requires predictions of how overland flow of surface water can be increased to rehydrate and revive downstream areas without causing unintended harms. We developed a biophysical flow rate expression (BioFRE) that relates shallow overland flow to roughness dominated by spatially variable vegetation and microtopography. Hydraulic theory was combined with vegetation and topographic field data to quantify hydraulic roughness without calibrating the expression to fit hydrologic data. To assess changes in overland flow capacity, we benchmarked BioFRE against best available simulations of the historic Everglades and against present-day hydrologic data representing various levels of degradation. The simulations revealed that overland flow capacity of the Everglades in now half of what it was historically in the Everglades primarily because of the loss of deepwater sloughs. The relative sensitivity of simulated flows to the individual biophysical factors was quantified and related to habitat value and drought and flood resilience. Our approach can potentially be used in other flowing wetland and floodplain systems to understand and adaptively manage water and ecological resources.