In NW Australia a range of emergent reefs bound the western margin of the Oceanic Shoals bioregion, but with the major feature
being numerous submerged shoals lying along and across the shelf edge. Scott Reef, the largest emergent reef system, has
a diverse shallow water coral reef ecosystem that has demonstrated impressive resilience to cyclone and coral bleaching
disturbances over the last 15 years (Gilmour et al, 2013). The adjacent deeper lagoon of South Scott Reef covers approximately
300 km2 in depths of 30-?70m. This deeper lagoon has areas of very high live coral cover and represents the largest example
of a mesophotic reef system in the region. The slightly deeper distribution of these habitats appears to have ameliorated
those impacts such as thermal stress and cyclones, which have caused significant disturbance to the adjacent shallow areas.
A spatial model using multibeam and seabed surveys with towed video and AUV in 2009 and 2011 has been developed by AIMS to
describe and predict the distribution of the key mesophotic habitats. While this model is the most advanced of its type
for such a reef system, additional research suggests that fine?scale water movement, including turbulence and upwelling
driven by internal waves, may be a key driver of these habitat patterns. We used the RV Falkor’s time at Scott Reef to
characterise these detailed oceanographic processes with the goal of integrating the physical and biological data to further
develop the spatial model, then extend this approach to other reefs and shoals in the region. The fine scale hydrodynamics
and their relationship to patterns of seabed biodiversity was explored from RV Falkor with intensive oceanographic measurements
of the water column across these features and detailed imaging transects of the seabed habitats using the SOI DDROV and
other camera gear.