Climate change is expected to significantly reduce water availability in the Murray-Darling Basin. This paper details a bio-physical economic model of the Basin regions which has been developed to estimate the effect of reduced water availability on irrigated agriculture. In the model, regions are linked through a network of water and salt flows, while crop yields respond to irrigation and salinity. The model allows water trade to be restricted to regions or to be unrestricted across the basin. The paper also develops a hypothetical scenario to demonstrate the model.