The flinging reef at Chiriatapu in South Andamans is a leeward channel reef and presents a topography which ensures substantial water residence time of about 30 days. Water from the open ocean enters the reef with moderate budgets of various chemical constituents across the reef bio-geochemical gradients develop in tune with the metabolic rhythm (Photosynthesis, respiration and calcification) of the biota. Organic carbon production, respiration and calcium deposition (gross and net production as inferred from carbon dioxide utilization are 4.25 and 0.56 gC m^-2d^-1 respectively, while the rate of calcium carbonate deposition is 1.3 gm^-2d^-1by the biota alter the oxygen and carbon dioxide content, as well as the salinity, together with various ionic species to produce alternate zones of varying chemical speciation. These gradients result from the distributional pattern of the biota. The salinity differential developed between the sea and the reef initiates salt wedges, leading to circulation dynamics and exchange of water. This brings a fresh load of salt and nutrients into the reef, completing the biogeochemical cycling. The various factors controlling the circulation pattern has been considered, and a modi€ ed mathematical model has been proposed for the ecosystem. This provides a framework for the study of the various subsystem controls, and their integration into a unit system model, based on environmental parameters and coordinated Community dynamics.