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Water is a contaminant that can lead to fuel system icing, microbial contamination, corrosion and fuel quantity gauging problems and therefore an efficient water management system is required in order to maximise the performance of an aircraft's fuel system. This paper describes a time-transient aircraft fuel tank model with water contamination, due to the principal mechanisms of dissolution, suspension, condensation and transportation. The tank model presented is a component of the NEPTUNE fuel system model which was developed for Airbus using the A380 as an example aircraft. A description of the physics of water contaminated fuel is given and of how this has been incorporated into a mathematical model of an aircraft fuel tank. A modular approach is demonstrated which enables interconnecting fuel tanks to be configured in larger systems in a flexible and easily understood manner.