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The Araruama lagoon water quality has deteriorated at an accelerated pace during the last decades, mainly due to an expansion of urban occupation. The nutrients input increased by domestic effluents could reach eutrophication, which may cause episodes of algal blooms and fish mortalities. The aim of this study was to evaluate the stratification of water parameters in the same sampling campaign. Eleven water samples were collected at the surface, middle, and bottom along the lagoon. For each sample, the following parameters were analyzed: biochemical oxygen demand (BOD5), dissolved oxygen (DO), turbidity, particulate organic carbon (POC), nitrogen and phosphorus (dissolved and particulate). The hydrodynamic characterization showed that regardless the connection with the ocean, a large part of the lagoon is more influenced by winds than tides. In general, parameters showed a homogeneous behavior along the water column. The results of DO and BOD5 confirmed that the lagoon is highly oxygenated. High phosphorus values combined with the result of the rates of nitrogen to phosphorus ratio (N:P) show that P is the limiting factor. The concentrations of BOD5, total nitrogen and total phosphorus, chlorophyll-a and phaeopigments corroborate this result.