The marine programme at FERAL integrates research, conservation, and education across India's coasts and offshore waters. A key ongoing effort is a long-term bioacoustics monitoring project off the Lakshadweep coast, a collaboration with The Habitats Trust (THT), Ashoka University, Woods Hole Oceanographic Institution (WHOI), Wavelet, and the University of Trans-Disciplinary Health Sciences and Technology (TDU), aimed at understanding cetacean distributions, oceanographic processes, and soundscapes. The programme also assesses the status of highly threatened coastal cetaceans within an Important Marine Mammal Area (IMMA) off India's West Coast. Past work has spanned traditional and artisanal fisheries, as well as monitoring sharks and rays along both coasts.

At its core, the programme prioritises scientific rigour to drive conservation on the ground, while building interdisciplinary capacity. It supports people through technical training workshops, internships, and PhD programmes. With the integration of the Islands and Reefs programme, the scope is expanding from coastal systems to island ecosystems and offshore waters, addressing some of the most data-poor and ecologically critical marine habitats in the Indian Ocean.