The Biscayne and Southern Everglades Coastal Transport(BISECT) model combines a three-dimensional groundwater model with a two- dimensional hydrodynamic surface-water model with variable-density solute-transport. BISECT was constructed by combining two existing models, Tides and Inflows to the Mangrove Everglades (TIME) (https://doi.org/10.3133/sir20075010), and Biscayne (https://doi.org/10.3133/sir20125099), and modifying the Flow and Transport in a Linked Overland/Aquifer Density-Dependent System (FTLOADDS) simulator (https://doi.org/10.1016/j.jhydrol.2005.04.015) to include spatially variations in the solar radiation reflected back into the atmosphere from the Earth’s surface (albedo) to improve model results. Input data files, containing parameters and boundary condtions for groundwater and surface-water, were developed for the calibrated model, representing conditions from 1996 to 2004. Input data scenarios were developed by altering the relevent parameters to represent the likely effects of 1) different depth aquifer barriers, 2) possible future changes to current water-management practices, and 3) two values of sea-level rise. Output files indicate the effects of these input on surface-water stages and flows, hydroperiod, and groundwater levels and salinity. Additional input and output files for the model was tested for sensitivity by perturbing the parameters for frictional resistance, wind forcing, tidal amplitude, thickness of surfical transistion layer, conductance of canal beds, vertical and horizontal aquifer conductance, and albedo. This USGS data release contains all of the input and output files for the simulations described in the associated model documentation report (https://doi.org/10.3133/SIR20195045). This data release also includes (1) postprocessing Fortran scripts and associated input data files for the sensitivity and scenarios runs, (2) the FTLOADDS source code.