The 2020 National Defense Authorization Act (NDAA) prohibition of PFAS-containing AFFF fire protection systems by 2024 has motivated the U.S. Department of Defense to study other alternatives. In this study, the current low-expansion AFFF foam fire suppression systems with trenches layout in NAVFAC facilities are modeled as water-based systems to determine the scale, coverage, and extinguishment times that can be expected from such systems. A reduced spacing of the trenches is then simulated to determine how spacing of the floor nozzles affects fire suppression and control. Additionally, a model of a previously identified floor-level low-pressure water mist nozzle with the incorporation of trenches is studied to validate its possibility of being a replacement option for the current NAVFAC systems. Each simulation consists of three components: fire model, sprinkler/water mist model, and extinction model. Each model is evaluated separately before inputting into the final simulations to determine the most accurate representation and minimize uncertainties. The final simulations with sprinkler nozzles show successful extinguishment up to 23 MW and better performance at earlier activation time and in setups with the current trench spacing. Little to no difference is observed between the two fuel spill fire scenarios at the same activation time and trench spacing. On the other hand, the low-pressure water mist systems do not meet adequate performance in the final hangar simulations.