These data include input and output files from the Gulf of Mexico Atlantis model. The simulations are published in Dornberger et al., 2019. The dataset includes every file needed to recreate the simulations: 1) the 18 spatial forcing files needed to recreate the sensitivity analysis; these vary the oil sensitivity threshold K, the fish oil threshold and the invertebrate oil threshold. The file naming scheme indicates parameter values used. 2) the three .prm files needed to recreate the different levels of fishing mortality (F=0.5, 1, 2.0, 10), The F rate indicates an increase in fishing mortality across all fishing sectors relative to baseline F=1 conditions, 3) seven detritus point-source input forcing .ts files corresponding to the Mississippi River input polygons discussed in the paper, 4) a complete Atlantis run folder set up to run the F=1 baseline scenario (1X base fishing mortality for all fleets) used in the paper (K1000, fish threshold 362, invert threshold 1000). Note, this folder contains a complete set of outputs files for the base case. The other runs (varying oil and fishing and detritus inputs) can be recreated by substituting the appropriate spatial forcing .nc, .prm and .ts files into this base case and re-running the simulation. This dataset supports the publication: Dornberger, L. N., Ainsworth, C. H., Coleman, F., & Wetzel, D. L. (2019). A Synthesis of Top-Down and Bottom-Up Impacts of the Deepwater Horizon Oil Spill Using Ecosystem Modeling. In S. A. Murawski, C. H. Ainsworth, S. A. Gilbert, D. J. Hollander, C. B. Paris, M. Schlüter., Wetzel D. (Eds.), Deep Oil Spills - Facts, Fate and Effects (pp. 536-550). Springer International. doi:10.1007/978-3-030-11605-7_31