Stuart is a senior member of the Australian Rivers Institute at Griffith University and, until July 2022, was the founding Director. His major research interests are in the ecology of river and wetland systems with a particular focus on the science to underpin river management. Stuart has had a full-time research leadership role since 1994 and has developed and led major national collaborative programs, often involving multiple institutions and interdisciplinary teams. He has extensive experience working with international and Australian government agencies and industry on water resource management issues and has been an active member and chair of state and national science advisory committees. Throughout this career, he has also maintained an active engagement with community-based groups working in natural resource management.

Stuart is currently a member of the Murray-Darling Basin Authority and has previously served as a National Water Commissioner and as a Director of Land and Water Australia. In 2019, he was appointed to the Earth Commission, hosted by Future Earth, and in 2022 was elected as a Fellow of the Australian Academy of Science.