During austral summers 2015/16 and 2016/17, unprecedented back-to-back coral bleaching events occurred along the Great Barrier Reef. Understanding the mechanisms controlling thermal variability is important for predicting thermal stress on marine ecosystems. The Central Great Barrier Reef has reef passages along the outer shelf, where intrusive upwelling allows for cool water to enter along the seafloor, providing potential relief for benthic ecosystems. Intrusive upwelling is associated with uplift and strengthening of the East Australian Current. Results are synthesized from long-term moorings, multiple Slocum glider deployments and a regional hydrodynamic model to document the subsurface thermal variability during the anomalously warm summers. As sea surface temperatures rose during summer, episodic periods of cooling occurred along the bottom. These upwelling events tended to take place with weakening southeasterly trade winds, weak winds, or northwesterly wind bursts and were associated with a poleward intensification of the along-shore currents. In Palm Passage, intrusions led to bottom cooling of 1 - 4°C over time scales of one week. In 2015/16, summertime warming near the surface exceeded temperatures over the mooring record, with a peak in February 2016, and cooler bottom temperatures were present until late-February 2016. While the passage of Tropical Cyclone Winston was associated with near-surface cooling in March 2016, bottom temperatures warmed by 4°C at 70 m depth within the passage. In 2016/17, outer shelf, near-surface temperatures reached similar magnitudes as in 2015/16, with multiple peaks from late-January 2017 to mid-March 2017. Southeasterly wind events, including the passage of Tropical Cyclone Debbie in March 2017, were associated with cooling of near-surface temperatures and greater amplitude warming of bottom temperatures. Relationships are determined between the subsurface thermal structure, ocean currents, and winds, offering insight into cross-shelf exchange processes adjacent to a western boundary current.