Across the globe, fish living on coral reefs have become increasingly more exposed to several threats including overfishing, pollution and habitat loss from climate change and ocean acidification. Significant damage caused to a reef often has serious consequences on the ability for many fish species to survive there. Biodiversity of reef fish is often a good measure of reef health and can be used to assess how the health of a reef is changing over time. The reef fish monitoring programme established by the Roctopus ecoTrust aims to provide information on the health status of reefs around Koh Tao by monitoring trends in the biodiversity of reef fish, as well as population trends for key reef species. This programme also aims to identify specific threats that local reefs are subject to, and the effect these are having on local reef fish communities.

Marine debris is often carried by winds and ocean currents to shallow bays and coves, where it commonly settles on nearby reefs. This can cause significant damage to coral structures and other reef associated organisms. The Roctopus ecoTrust organise weekly beach cleans in order to minimise levels of trash that may be carried onto local reefs. Roctopus contribute data to the Clean Swell project established by Ocean Conservancy, a science-based organisation that seeks solutions for a healthy ocean and wildlife that depends on it.

It is estimated that between 5-10 million tonnes of trash enter our oceans each year, the majority of which is plastic. Some types of plastic take hundreds of years to decompose. During this time, they have the potential to cause significant damage to coral reefs and the organisms that live there. The Roctopus ecoTrust conduct regular underwater reef cleans around the island, removing trash items that are likely to cause damage to local reef ecosystems. Roctopus are active members of the non-profit marine conservation organisation Project AWARE, and contribute data to their Dive Against Debris program. This program aims to prevent the accumulation of trash in marine environments by working with volunteer divers all across the world.

During their adult life stages, Crown of Thorns starfish (COTs) are corallivores and predate on the live polyps of hard corals. If the density of COTs increases within a particular area, the mortality of corals through COT predation may exceed the rate at which new corals are able to recruit in the same area. This may lead to a significant loss of hard corals within a reef ecosystem. In the last 100 years, COTs outbreaks have increased both in severity and frequency throughout the world and these outbreaks have commonly been associated with anthropogenic influences. Research projects established by the Roctopus ecoTrust aim to monitor the population density of COTs, and identify areas where outbreak populations may form.  Research is also conducted on the habitat and dietary preferences of COTs in order to improve our understanding of the ecological effects of high COT densities around Koh Tao.