As water demands continue to grow, South Africa is starting to consider seawater desalination as a potential future supply source, and it is currently being investigated at a feasibility level in a number of coastal cities, including Cape Town. Desalination is different to conventional surface and groundwater supply sources in that it is climate-resilient, having an assurance of supply of essentially 100 percent. However, the increased reliability comes at a great cost. This paper presents a methodology developed for modelling a proposed desalination plant as an integrated component of the Western Cape Water Supply System, in order to optimise system operating rules and cost. The modelling entailed short-term and long-term system analyses in the Water Resources Yield Model and Water Resources Planning Model, and estimation of first-order capital and operating costs in order to calculate and compare Unit Reference Values. The maximum increase in yield was found to occur when the seawater desalination plant is used as a base supply, operational all the time. There was little benefit, in terms of system yield, in using the desalination plant as an emergency supply source only. Unit reference values for the desalination plant decrease as the percentage supply from the plant increases, meaning that the lowest possible cost per cubic metre of water supplied is when the desalination plant is used as a base supply. It was also apparent that the unit reference values decrease with an increase in desalination plant capacity, suggesting that, from an economic perspective, the optimal solution would be to have one large desalination plant operational immediately.