Scott's research focuses on how and why productive reef ecosystems collapse into impoverished low-value systems that can be difficult to reverse. He is interested in defining critical tipping-points and early-warning signs for reefs exposed to increasing, but ostensibly manageable, human stressors including overfishing, invasive species and urbanisation in combination with climate change. Scott's research approach is founded on a strong understanding of natural history gained from extensive SCUBA-based surveys at biogeographical scales and critical field experiments to reveal key mechanisms driving reef ecosystems. 

Scot is a contributor to the Maria Island Marine Reserve Observatory.

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