Ecosystem Based Management (EBM) essentially requires a coordinated effort and for effective management, in depth understanding of the complex processes and the interactions within and between the ecosystems matters. Marine Living Resource Programme (MLRP) of the Ministry of Earth Sciences (MoES), India, implemented through Centre for marine Living Resources and Ecology (CMLRE), was aimed to develop better understanding of the ecosystems of the Indian Exclusive Economic Zone (EEZ) through regular monitoring efforts. This work is a compilation on the understanding of the ecosystem processes governing the Arabian Sea, Bay of Bengal, and the Andaman waters including its biological and biogeochemical response through studies taken up since the inception of MLRP in 1998. The outcomes of the programme provided a baseline information on the ecosystem dynamics and ecological interactions and the vast resources existing in and around the EEZ. The sustainable utilization of these resources is indispensable in the context of Sustainable Development Goals (SDG 14), to maintain the health of the ecosystems. Regardless of the information available, further sustained long-term observations with high temporal and spatial resolutions along with experimental studies, high-resolution modeling efforts and using advanced techniques and methods, are suggested for the future. This is essential to strengthen the understanding of the ecosystems and to develop predictive capabilities and assessments towards building efficient management strategies for the sustainable utilization of the marine living resources.