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Large-scale models play a key role in determining long range flow pathways from continental interiors to the oceans, yet struggle to simulate the local flow patterns offered by small-scale models. We have developed a highly scalable numerical framework to model continental groundwater flow which capture the intricate flow pathways between deep aquifers and the near-surface. The coupled thermal-hydraulic basin structure is inferred from hydraulic head measurements, recharge estimates from geochemical proxies, and borehole temperature data using a Bayesian framework. We use it to model the deep groundwater flow beneath the Sydney\u2013Gunnedah\u2013Bowen Basin, part of Australia\u2019s largest aquifer system. Coastal aquifers have flow rates of up to 0.3 m/day, and a corresponding groundwater residence time of just 2,000 years. In contrast, our model predicts slow flow rates of 0.005 m/day for inland aquifers, resulting in a groundwater residence time of 400,000 years. 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