[Truncated abstract] The Collie River drainage basin is an important water resource catchment in southwestern Australia. Salinisation of a major water supply within the catchment, the Wellington Reservoir, has arisen due to changes in the water and salt balance in response to land clearing over saprolite aquifers. Paired catchment studies, the Collie Experimental Catchments (CECs), established in the early 1970’s in high and low rainfall areas increased our understanding of water and salt (predominantly chloride) movement in these aquifers through the collection and analysis of high resolution spatio-temporal data. However, the conceptual models developed from this work take little account of landscape heterogeneity, and this has caused problems in subsequent modelling studies, where success in calibrating stream flow has been countered by difficulties in predicting salt loads. The challenge remains to better describe variability in the Collie landscape and understand the influence of climate, vegetation, geology and geomorphology on observed water and salt fluxes. The release of salt from the lower saprolite aquifer and the role of the surficial aquifer in buffering groundwater discharge were investigated. The acquisition, analysis and interpretation of new regolith and geophysical data in 2001-2003 from the CECs, together with data from a high resolution digital elevation model, and existing drilling information, were used to construct a geologicalgeomorphological compartment framework, to observe changes in aquifer behaviour ... Significant differences in the salt flux from compartments have been noted at a range of scales, with implications for both water resource and land management. The approach developed to identify compartments and assess their efficiency could be simplified, using catchment critical parameters determined from geological and geomorphological characteristics. As a consequence, the implementation of a compartment framework in catchments with saprolite aquifers should allow for more informed decisions to be made in the selection of sites for revegetation strategies or the development of engineering works. This is particularly important in the Collie Catchment where reclamation scenarios are currently being discussed. Consideration of the catchment as a compartmentalised system would help manage salt loads in the Collie River and return the Wellington Reservoir to a functional water resource.