Coastal lagoons are transitional zones between land and sea: they are shallow inland water bodies, separated from the ocean by a barrier, but connected to it by one or more restricted inlets which remain open at least intermittently. Coastal lagoons are recognized world over for their ecological and economic value due to their contributions to agricultural, tourism industries, and fishery sectors. Ironically, however, they are also the most exploited water bodies through anthropogenic pressures which in turn affect the plants and animals inhabiting these areas. Sustainable management and restoration of such vulnerable ecosystems become the foremost challenges for the ecosystem managers. Chilka Lake, Asia's largest brackish water lagoon and a Ramsar site, is no exception. Chilka lagoon has been under considerable threat ecologically over the last two decades or so, and developing sustainable management strategies for the lagoon required a concerted study involving physical, chemical, and biological investigations at the ecosystem level or ecological modeling. In the present research held for period 5–6 years (2004–10), a Lagrangian approach was made to addressing some major issues concerning the lagoon such as factors that sustained the ecosystem so far and its further evolution. Such interdisciplinary approaches should help answer several ecological questions say, “when does large-scale hypoxia occur?” in such water bodies and what are the measures needed to avoid hypoxic events, etc. In the present study, we have made an attempt to understand the changes associated with biogeochemical cycles in the lagoon especially the dissolved oxygen and net ecosystem metabolism events. The study presented here unifies the physical/chemical/biological processes obtainable through monitoring the Chilka Lake via sound field observations with a modeling approach which is the essence of this study. © 2018 Elsevier B.V.