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AbstractThe Murray-Darling Basin Salinity Management Strategy (BSMS) aims to control natural salt loads and the rise in land use change-induced salt loads in the River Murray and tributaries, and protect key natural resource values. Many cities and towns in South Australia source between 50% and 100% of their water supplies from the River Murray, and increasing salinity has major cost implications for infrastructure, as well as for potable water quality. The BSMS recognises that measures to counter salinity such as water use efficiency and revegetation will take decades to become effective, hence the need for large scale groundwater pumping schemes to intercept saline inflows. The BSMS and various State legislation and strategies require the use of models to quantify salt loads to the River and to attribute accountable actions to the appropriate responsible parties. Salinity Registers track the balance of the debits and credits, to manage future changes in salt loads. This paper demonstrates how groundwater modelling is an effective tool for both quantifying and optimising the design and operation of salt interception schemes, and also for differentiating the flow contribution and timing of saline inflows due to natural flows and changed land use impacts. Thus modelling can inform the process of quantifying contributions due to the “legacy of history” (ie. pre-1988 impacts) and due to “future impacts” (post-1988 accountable actions).