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Sustainability of irrigated agriculture in the semi-arid regions such as the rice growing regions of the southern Australia could be under serious threat due to recharge to saline groundwater leading to secondary salinisation. This paper presents two approaches to reduce net recharge to shallow saline groundwater from ponded rice cropping systems using a soil, water and groundwater management model-SWAGMAN model. First approach applies the concept of growing deep-rooted crop (crop consuming water from soil and shallow water table) over an area equivalent to recharge from a unit area of rice crop to maintain the total water balance. The second approach involves achieving whole farm water balance for average and wet climatic conditions to find out optimum cropping pattern to minimise recharge from rice based system. Results of both approaches are sensitive to water table depth and regional groundwater outflow rates. The first approach was applied to determine an optimal mix of rice/lucerne crop to keep water tables and average soil salinity changes less than 0 m/year and 0.015 dS/m, respectively. The area of lucerne required to match the net groundwater rise caused by 1 ha of rice is 1.27, 2.45 and 3.55 ha for 1, 0.5 and 0.2 ML/ha regional groundwater outflow capacity. Results from second approach revealed that it is possible to control net recharge under above average rainfall using a suitable whole farm cropping mix e. g. 50 ha rice-wheat rotation, 19 ha rice, 25 ha of lucerne and 136 ha of fallow.