There is much uncertainty associated with water accounting in the complex lowland parts of the river systems across the Murray Darling Basin (MDB), where diversions and extractions, losses to flood plains and wetlands and groundwater recharge can all occur within the same reach and at the same time. Flood plain losses include water harvesting and overbank flow going to the wetlands and subsequently being evapotranspired. This water is generally not metered and hence there is no good quality historical data available. Monitoring and quantifying these losses are challenging. Modeling the processes causing these losses on the flood plain is an alternative way of quantifying these losses. This paper presents a simple water loss accounting model that tracks water and quantifies processes occurring on a flood plain in a river reach (Figure 1). These include diversions for irrigation, on-farm storage (OFS) and use, flood plain harvesting, overbank flow to the wetlands and return flow to the river. Given initial estimates of such parameters as irrigation efficiency, OFS volume and area, overbank flow threshold and fraction of return flows, optimum values of these parameters are found by minimising the residual error term for the water accounting period. The model attributes some of the unaccounted losses to flood plain water harvesting to the on-farm storages for later use, and estimates return flows from the wetlands and irrigation areas.