Given the population increase in the catchment to Chilika Lake and the related changes in land use policies, agricultural practices, and water resource management, this lake has been subjected to increasing anthropogenic influence. As a consequence, the unique biodiversity and primary production within the lagoon decreased, while eutrophication and siltation increased. As a counter-initiative it was decided to artificially open the lake to the sea by dredging. To help trace and quantify the anthropologic effects on Chilika Lake, a combined sedimentologic, chemical, and isotopic study of the lagoon and its sediments is in progress. The results from two campaigns during the monsoon and consecutive dry season suggest that the large gradients in salinity, sediment and nutrient inputs, as well as primary productivity within the lagoon are controlled by variable fluxes of water, sediment, and nutrients from the three separate catchments to the lagoon. Trends in changes of salinity, H- and O-isotope compositions of waters, but also of concentrations and C- and/or N-isotope compositions of the dissolved inorganic carbon (DIC), particulate organic matter (POM), and aquatic plants indicate that mixing in the lagoon occurs between new freshwater inputs and evaporated water within the basin itself. Except for the outer channel, mixing with seawater is limited. In contrast, the C-isotope compositions of the organic matter in the sediments support a higher overall proportion of “marine” or estuarine POM during the past. The latter may be important during the dry season, coupling salinity increase to the changes in DIC and POM carbon isotope compositions. The salinity, DIC, H-, O-, and C-isotope compositions of water are compatible with evaporation as the main driver for a salinity increase, rather than admixtures with seawater.