Intrusion of deep Coral Sea water onto the central Great Barrier Reef (GBR) shelf is a critical mechanism that allows for cool and nutrient-rich waters to enter the Great Barrier Reef lagoon. These cross-shelf exchanges enhance primary productivity, influencing the distribution of marine organisms from plankton to top predators, and may alleviate the severity of coral bleaching during marine heatwaves. We combine a 15-year observational dataset with a 12 year hydrodynamic and biogeochemical model hindcast of the region (eReefs GBR4) to reassess the key drivers behind its occurrence. We demonstrate how these simulated and observed datasets allow for the characterisation of seasonal and inter-annual variability of these events and thus enable the evaluation of trends and regime shifts in the continental shelf water intrusion patterns. Insights from this comprehensive analysis can guide evidence-based decisions aimed at mitigating the impacts of environmental changes on the central GBR, thus aiding the conservation and sustainable management of the GBR World Heritage Area.