The ecology of sea cucumbers, their ecological role in marine ecosystems, and the potential impacts of their removal (through over-fishing) was the subject of this study. Cage experiments suggested that sea cucumbers are beneficial for seagrass, with significantly higher seagrass productivity under natural densities compared to exclusion areas. Conversely, the presence of sea cucumbers appeared to reduce microalgae biomass. Sea cucumbers influenced only the top 6 cm of the sediment during their feeding and burying activities. Differences in the animal’s behaviour were strongly related to water temperature, thus resulting in drastic seasonal changes. Hence, over-fishing of sea cucumbers might alter the overall habitat structure in unpredictable ways and could thus have ecological consequences for tropical seagrass beds in the long term.