Sea cucumber fisheries have expanded globally due to increased demand for these products as luxury food items and pharmaceuticals. Recent studies have highlighted the importance of sea cucumbers’ role in tropical reef ecosystems, as daily feeding behaviour cleans reef sediments and suppresses microbial pathogens, supporting reef health and improving the growth of local seagrass beds. Sustainable sea cucumber fisheries management is impacted by a poor understanding of commercial species ecological and biological traits, with key stock assessment components often extrapolated from non-local populations, or a different species altogether. Here we present a novel method to advance the sustainability of sea cucumber fisheries, using local-scale independent survey data and species distribution models (SDMs) to improve stock biomass estimates. Specifically, we examine the habitat suitability for Stichopus herrmanni and Thelenota ananas that are commercially harvested by the Queensland Sea Cucumber Fishery on the Great Barrier Reef, in relation to ten environmental predictors (i.e. depth, slope, sea surface temperature, salinity, current, geomorphic zone, benthic habitat, sedimentary components including bulk carbonate, sand and gravel proportions). Results showed that depth, bulk carbonate concentrations in sediment, and sea surface temperature were the main drivers of habitat suitability between the two species. Predicative distribution maps revealed differing patterns of habitat suitability, particularly in their latitudinal distributions. This study shows that SDMs can be used to estimate sea cucumber biomass based on the proportion of suitable habitat, at an ecosystem scale, applying conservative estimates to fisheries management, as well as identifying biologically important areas of conservation priority.