This dataset includes outputs from an ecosystem model, which is a tool for regional science managers to explore marine spatial planning scenarios in the context of static and dynamic environmental covariates. The dataset includes predicted fish biomass from the Ecopath with Ecosim and Ecospace model set up over the Florida Reef Tract, during eight scenarios and across 36 trophic groups the time period between 1994 and 2012. Simulations considered all pairwise combinations of changing the size of Marine Protected Areas (‘existing MPAs’, ‘large MPAs’), and varying rates of movement via modeled diffusion (‘low diffusion’, ‘high diffusion’), and increasing fishing effort (total effect multiplier; ‘low TEM’, ‘high TEM’).