A two-dimensional model is used to study transport of material within Myall Lakes and is coupled to the ocean using a one-dimensional model of Lower Myall River. Runoff from the catchment is calculated from water levels and compares favourably with rainfall assuming an average runoff yield of 28% and a runoff coefficient of 47% for events above the 90th percentile. Most of the runoff enters Bombah Broadwater which is also the only basin connected to the ocean. Intermittent runoff events rapidly displace water from Bombah Broadwater into Boolambayte Lake and from Boolambayte Lake into Myall Lake. Displaced water is mixed within basins by wind-driven circulation within the time scale that levels fall as water drains from the lakes to the ocean. Only 7% of the nutrient load entering Bombah Broadwater becomes resident Myall Lake. About 40% of the nutrient load entering Boolambayte Lake becomes resident in Myall Lake. Median time scales for loss of conservative material entering each basin with the runoff are: 140 days for Bombah Broadwater, 118 days for Boolambayte Lake, and 535 days for Myall Lake. Salinity fluctuates greatly in Bombah Broadwater but is stable in Myall Lake. Material loss from Bombah Broadwater is characterized by many time scales associated with runoff from the catchment and low-frequency changes in ocean water level. Comparison of observed distributions of total nitrogen with simulations indicates that there are sources of total nitrogen in Boolambayte Lake and Myall Lake and sinks of total nitrogen in Bombah Broadwater. There appear to be sinks of total phosphorus throughout the Myall Lakes.