Ecosystem monitoring is a critical component of any attempt to conserve our environment, whether it be on land or in the sea.  Monitoring, through rigorous scientific studies is the best way to determine if conservation actions or initiatives, such as establishing a Marine Protected Area, are having the desired effect on the environment you are trying to protect.  There are endless ways of conducting environmental research, and depend, in part, on the question trying to be answered, but generally they all come down to quantifying the number of organisms living in an ecosystem or their health.

SCUBA Surveys – Reef Check

Reef Check are SCUBA based surveys which use simple techniques designed to be run using citizen scientists without the need of formal marine science education.  The methods are standardized and run by organizations not only throughout the Philippines but across many other countries, allowing a comparison of data collected over vast areas of the world.


When we think of the ocean, the first thing we think of, for many people, is fish.  This is because they are one of the most abundant animals in the sea, they are highly mobile and very visible, and lastly, are a popular source of food all over the world. Due to their abundance, and their importance to human populations, monitoring fish populations is one of the most commonly used ways of assessing the health of a marine ecosystem.

Counting fish while using SCUBA is probably the most common technique used by marine scientists and conservationists to assess fish populations. Although many different methods of counting are used, here at The Coral Triangle Conservancy (CTC) we regularly conduct Reef Check fish surveys.


After fish, corals are probably the second organism people associate with tropical oceans. This is because they are the most abundant, colourful component of tropical reefs and are just generally hard to miss. Although they are not the only organism that makes up a tropical reef, they are one of the most common, and the most important, as they actively build the reef, not just live passively on it.

Although we don’t eat corals, many people rely on them for food indirectly, as they create the habitat, or home, for vast numbers of coral reef fish.  Corals, however, are sensitive to environmental changes, like nutrient input from agriculture and sewage, sediment from land clearing and temperature increases.  As such, monitoring the health of corals is an important way to assess the health of the whole coral reef ecosystem.

The Reef Check Surveys conducted regularly by Coral Triangle Conservancy, also collect data on coral cover and health.  The Reef Check methods give a good although general indication of coral cover, types of coral present (based on a simple classification system) and the overall health. The Coral Triangle Conservancy however also conducts photo-quadrat surveys as part of the Reef Check surveys, as well as for other targeted monitoring programs.  Photoquadrat surveys involve taking a series of high quality photographs of a fixed area of seafloor (generally 0.25m2). These photos are then analysed on a computer to determine the composition of the reef.  Manual interpretation of benthic images to classify types of benthic cover is a time consuming and costly process.  However, this issue has recently been addressed by development of a number of automated or semi-automated benthic identification and classification systems.


Invertebrates (animals without a backbone), which include crabs, crayfish, molluscs, starfish and sea cumbers (to name only a few), are a vital component of coral reef ecosystems. In fact, there are far greater numbers of invertebrates on coral reefs than vertebrates (i.e. fish), both in terms of biodiversity (numbers of species) and absolute number of organisms.  Invertebrates, other than corals, are often overlooked by many casual observers of coral reefs, due largely to the distraction of highly visible and colourful array of fish and corals.  However, they should not be overlooked by any attempt to determine the health or status of a coral reef, as they are such an important part of the reef ecosystem.

CTC regularly conducts Reef Check Surveys which include an assessment of commercially valuable invertebrates which are often targeted by fisheries.  The target invertebrates include lobsters, giant clams, triton snails, sea cucumbers and sea-urchins.

Towed Video Mapping and Manta Towing

Although it is important and fun to get in the water and SCUBA dive coral reefs to really understand them, it can be costly and slow to conduct surveys using SCUBA.  Due to the time and cost restrains, the area covered by SCUBA surveys is generally quite restricted.  To assess reef health over broad areas there are a few techniques that can be used including towed video mapping and manta towing.

Towed video mapping uses a live-feed video camera to display in real time the habitat and corals under a boat. This is combined with Global Positioning System (GPS) information to generate a map of the types of benthic habitat, their density and health.  Manta towing is similar to towed video, but instead of a camera, a snorkel diver is very slowly towed by a boat and the diver can record information about the habitats observed.

Mangrove Surveys

There are numerous ways which the health and status of mangroves can be assessed. Mangroves often cover extensive areas of shoreline and as such, are often affected by the large scale impacts such as shoreline clearing or land reclamation.  As such, one of the key monitoring tools is mapping, which can survey extensive areas of mangroves for changes, with the least amount of expense or manpower.

Mangrove mapping uses areal imagery, either captured by satellite, plane or drone, to determine the extent of mangrove habitat.  The area occupied by mangroves can be then tracked through time, even back in time, when historical areal imagery is available.

Although mapping is a powerful tool, it is not perfect, and interpreting imagery can be a complicated process. Furthermore, areal imagery only gives a very broad picture of mangrove health.  Ideally it should be combined with ground truthing, whereby mapped areas are checked by field teams for accuracy.  These field teams can also perform on-ground assessments of mangrove health by assessing parameters such as canopy cover, tree density and size and seedling density.

Seagrass Surveys

Similar to mangroves, broadscale assessment of seagrass can be conducted using mapping, although it is made more difficult due to seagrass being submerged.  This means that getting suitable aerial imagery is difficult as you need calm weather days and photographs with minimal sun glare.  However, with good quality imagery, it is generally possible to tell the location and extent of seagrass habitat from aerial imagery.  As with mangroves, mapping techniques are not perfect, and ground truthing is required, which in the case of seagrass, involves using either manta towing (towing a snorkeler behind a boat) or towed-video (towing a live-feed camera behind a boat) to validate the accuracy of the aerial maps.