Ecosystem level changes in water quality and biotic communities in coastal lagoons have been associated with intensification of anthropogenic pressures. In light of incipient changes in Asia’s largest brackish water lagoon (Chilika, India), an examination of different dissolved nutrients distribution and phytoplankton biomass, was conducted through seasonal water quality monitoring in the year 2011. The lagoon showed both spatial and temporal variation in nutrient concentration, mostly altered by fresh-water input, regulated the chlorophyll distribution as well. Dissolved inorganic N:P ratio in the lagoon showed nitrogen limitation in May and December, 2011. Chlorophyll in the lagoon varied between 3.38 and 17.66 mg m⁻³. Spatially, northern part of the lagoon showed higher values of DIN and chlorophyll during most part of the year, except in May, when highest DIN was recorded in the southern part. Statistical analysis revealed that dissolved NH$^{+}_{4}$–N and urea could combinedly explain 43% of Chlorophyll-𝑎 (Chl-𝑎) variability which was relatively higher than that explained by NO$^{-}_{3}$–N and NO$^{-}_{2}$–N (12.4%) in lagoon water. Trophic state index calculated for different sectors of the lagoon confirmed the inter-sectoral and inter-seasonal shift from mesotrophic to eutrophic conditions largely depending on nutrient rich freshwater input.