Increases in induced waterlogging and dryland salinization resulting from deep drainage to watertables have been predicted to occur across the mixed farming zone of northern Victoria. Consequently, deep-rooted perennials need to be introduced into farming systems. Lucerne (Medicago sativa) has been found to have a higher level of water extraction than annual crops and pastures. But one of the barriers to farmers adopting cropping with lucerne is that they fear their risk in production will increase and that their economic and financial benefits will be compromised. In this study, farm management systems where lucerne phase farming has replaced cropping with annual legumes were investigated. Changes in profitability and cash flow as a result of making the substitution were calculated and an assessment made of likely increases in business risk for the farming systems.