Malcolm began his research career in the 1980s as a fisheries biologist. He worked extensively on stock assessment of deepwater fish (in particular orange roughy), before broadening his research interests to more general deep-sea ecosystems. He studied seamounts for many years, and headed the Census of Marine Life on Seamounts, a major 6 year international research programme. His studies have involved a lot of time at sea; with over 70 surveys, including submersible dives, and international work in the Antarctic and southwest Pacific. Currently he leads NIWA research projects describing the biodiversity of deep-sea habitats, assessing ecological risk to these habitats and communities from fishing and mining activities, and ways to improve the management of environmental impacts.