One-dimensional simulation models of farming systems have been used to evaluate production and environmental aspects of farming systems, including the amount of deep drainage lost under crops and pastures. Most of this deep drainage is assumed to contribute recharge to groundwater. In addition, previous studies, most notably in the Liverpool Plains, have identified large anomalies between estimates derived using one-dimensional models of deep drainage lost below the plant root zone and recharge estimates based on hydrograph responses. In this paper we report the integration and application of a one-dimensional farming systems model (GrassGro TM ) into a catchment framework based on the USDA soil and water assessment tool (SWAT model) with enhanced allowance for lateral flows. The catchment framework was applied to the Hughes Creek sub-catchment of the Goulburn-Broken catchment, which has been identified by the National Action Plan for Salinity as a Victorian priority catchment. Simulation results were validated against three independent approaches: 1) predicted transpiration compared with estimates derived using the broad scale Zhang approach; 2) catchment averaged recharge estimates compared with recharge data embedded in the ABARE model based on the Catchment Characterisation groundwater conceptualisation project; and 3) observed stream flow data. Derived simulation results show good agreement between deep drainage estimates, observed stream flow and available experimental data. Reported results suggest that this framework can be used to assess the off-site impacts of land management decisions in a catchment context and can therefore extend the application of one-dimensional farming systems simulation models for assessing the potential impacts of salinity from agricultural land management.