The paper presents the development and evaluation of methods that estimate recharge and discharge, water flow, and salt fluxes in rivers. The methods in combination provide an inferential framework to predict dryland salinity and the selection of the appropriate management scenarios. Hydrogeomorphic Analysis of Regional Spatial Data (HARSD) was used for delineating hydrogeologically homogenous units, and to translate limited hydrological data into hydraulic head surfaces and ultimately a steady state flow net representing recharge-discharge relationships. A complex, physically based water, energy, and carbon model (WAVES) was developed and tested to provide recharge estimates required for the now net simulations. Remote sensing imagery and analysis techniques involving airborne, advanced very high resolution reflectance (AVHRR) and LANDSAT-Thematic Mapper (TM) data were used to infer the temporal and spatial patterns of leaf area index (LAI) and land-cover type. The techniques were applied in 22 subcatchments in the Loddon and Campaspe and for the two major catchments. Modeled recharge was consistent with local estimates based on inverse methods and with subcatchment-scale estimates based on stream salt leeds under a steady-state assumption. The calibrated flow nets for each of the subcatchment have been used to test the sensitivity of this system to changes in recharge resulting from land use change. It is shown, for example, that the Upper Campaspe subcatchment would require the reforestation of key recharge areas totaling 45% of the subcatchment to reduce salt loads from approximately 25 000 Mg yr(-1) down to 18 000 Mg yr(-1) under steady state assumption.