Ningaloo Reef is a World Heritage Area known for its coral, abundant megafauna, and the annual aggregation of whale sharks (Rhincodon typus). Despite its high natural and economic values, the underlying oceanographic processes supporting this diversity remain unresolved. We deployed a Slocum ocean glider from Sandy Bay to the south of Point Cloates in April/May 2017 to provide data on seawater temperature and salinity. We found significant differences to the north and south of Point Cloates. To the north, temperature and salinity was influenced by the warmer, lower salinity water of the southward flowing Leeuwin Current (≈28.2oC and 35.04). To the south, temperatures were lower and salinity was higher (≈27oC and ≈35.2), due to the northward-flowing, Ningaloo Current. Most notably however, we identified multiple instances of dense shelf water transport (DSWT) that were not observed in the north. Horizontal density gradients reached 0.07 x 10-5 kgm-4 southwest of Point Cloates, similar to those measured around Australia. The presence of DSWT in Ningaloo is significant as they are known to enhance local productivity through the resuspension of sediments and nutrients by cross-shelf currents. Thus, DSWT may be an important but overlooked process that supports the diversity of the southern Ningaloo reef.