© 2019 Author(s).The formation of the Paraíba do Sul river delta plain on the coast of Rio de Janeiro state, Brazil, gave rise to diverse lagoons formed under different sea level regimes and climate variations. Sedimentary core lithology, organic matter geochemistry, and isotopic composition (δ13C and d15N) were analyzed to interpret the sedimentation of the paleoenvironment of the Lagoa Salgada carbonate system. Different lithofacies reflect variations in the depositional environment. The abundance of silt and clay between 5.8 and 3.7 kyr enhances the interpretation of a transgressive system, which promoted the stagnation of coarse sediment deposition due to coast drowning. Geochemistry data from this period (5.8-3.7 kyr) suggest the dominance of a wet climate with an increase of C3 plants and a marked dry event between 4.2 and 3.8 kyr. This dryer event also matches with previously published records from around the world, indicating a global event at 4.2 ka. Between 3.8 and 1.5 kyr, Lagoa Salgada was isolated; sand and silt arrived at the system by erosion with the retreat of the ocean and less fluvial drainage. Geochemistry from this moment marks the changes to favorable conditions for microorganisms active in the precipitation of carbonates, forming microbial mats and stromatolites in the drier phase.