Ships cruising across the seas have to make sure of ample freshwater supply for the passengers. In this paper, a desalination technique using Multi-Stage Air Gap Membrane Distillation (AGMD) has been proposed to obtain freshwater with the waste heat recovery from a marine engine for on-board ships. The simulation was performed based on the experiments conducted on a lab-scale multi-stage AGMD unit. The seawater to cool marine engine is considered to be the feed solution while the sea surface water is selected as the coolant. The geographical distributions of sea surface salinity and temperature have been considered in the simulation. Effect of the process parameters including the temperature of engine cooling water and sea surface water, air gap thickness, and seawater salinity has been investigated. A transport model has been used to predict the distillate production rate and numbers of MD modules. It is found that this process combined with the ship's engine cooling water could provide a Specific Energy Consumption (SEC) range between 1.58 and 2.63 kWh/m3 for a freshwater demand between 1 to 15 m3/day, considering the pumping energy only. The optimum feed temperature range is found between 65°C and 70 °C for an exit temperature limit of 40 °C.