Seagrass meadows in the Torres Strait provide significant foraging grounds for green turtles and dugongs, two culturally significant species for local communities. Dramatic declines in seagrass meadows in western Torres Strait were recorded in 2019 and 2020. In response to understanding the drivers of change directly related to these seagrass declines, James Cook University, Mabuyag Rangers, the Torres Strait Regional Authority’s Sea Team and Goemulgaw PBC co-designed a study to understand to what extent grazing by megaherbivores (green turtles and dugongs) is driving seagrass decline. Megaherbivore exclusion cages were used in two key meadows with differing seagrass communities at Mabuyag Island and Orman Reefs, to understand the impact of green turtle and dugong grazing on seagrass structure. The experimental set up and sampling was co-delivered with all study partners and in consultation with the local community. Megaherbivory was shown to be an important structuring influence in both seagrass meadows but to differing degrees, influencing seagrass biomass and canopy height. These results, combined with other investigations into seagrass declines, inform Traditional Owner led dugong and turtle management plans and help direct actions for remediation as required by both Traditional Owners and management agencies.