In the Central Great Barrier Reef, the outer continental shelf has an open reef matrix that facilitates the exchange of waters with the Coral Sea. During austral summer, cool water intrudes onto the shelf along the seafloor. Temperature observations reveal cool, bottom intrusions during a 6 year period from the Queensland Integrated Marine Observing System's Palm Passage mooring. A metric is used to identify 64 intrusion events. These intrusions predominantly occur from October to March including the wet season. During an event, the outer‐shelf's near‐bottom temperature decreases by 1–3°C typically over 1 week. The near‐bottom salinity tends to increase, while near‐surface changes do not reflect these tendencies. Intrusion events occur predominantly with either weakening equatorward winds or poleward wind bursts. A regional hydrodynamic model for the Great Barrier Reef captures the timing and amplitude of these intrusions. During intrusion events, isotherms tend to uplift over the continental slope and onto the shelf and the East Australian Current intensifies poleward. Over the shelf, a bottom‐intensified onshore current coincides with bottom cooling. For numerous events, the model diagnostics reveal that the cross‐shelf flow is dominated by the geostrophic contribution. A vertical circulation tilts the isopycnals upward on the southern side of the passage, causing an along‐shelf density gradient and geostrophic onshore flow with depth. While wind fluctuations play a major role in controlling the along‐shelf currents, model results indicate that a concurrent topographically induced circulation can assist the onshore spread of cool water.