One of LINI’s main activities is to conduct coral reef surveys. These surveys help us to assess the health of the reefs and reef fisheries resources at the beginning of each project, and to show any changes and improvements as the project progresses. A number of survey methods are used, including 'manta tows' and line transects. Line transects and visual census are used for monitoring fish populations and diversity, while other methods are used for more general fisheries surveys. LINI staff are very experienced in conducting these surveys, and in fish identification.

LINI has a database containing extensive information about the marine resources in areas where reef fish are collected for the marine aquarium trade. These data are from Buleleng district, Bali, Lampung in Sumatra , the Pangkajene Islands in South Sulawesi, and the Banggai Islands  in NE Sulawesi. LINI has also assisted the department of fisheries in the development of its own aquarium fisheries database.