The watershed of a large tropical coastal lagoon, historically hosting large sugarcane crops, which has been reduced during the last decades. It suggests that land use and land cover changes (LULCC) would lower the trophic state of the coastal lagoon due to less fertilization application and consequently reducing nutrient transfer into the lagoon. In this context, this study assessed the influence of LULCC, represented by the reduction of the sugarcane crops on the trophic state of a large tropical coastal lagoon. This influence was assessed by means of information about the long-term overall mass-balance budget, involving the estimation of the N and P loads from the sugarcane crops, other anthropogenic sources and natural processes; measurements of the river N and P fluxes into the lagoon; its seaward outflow and the long-term lacustrine nutrient retention. The results indicate that sugarcane crop reduction represented a decrease of 686 t of N and 51 t of P being emitted to the lagoon watershed. However, N and P loads from sugarcane crops were partially replaced by other anthropogenic activities, but even with the reduction of the nutrient fluxes, the long-term supereutrophic responses of the coastal lagoon was maintained. The sediment-related C/N and isotopic composition of the lagoon was sensitive to LULCC, indicating changes on the organic matter inputs into the lagoon. The trophic state was also influenced by the soil N and P accumulation and the long-term nutrient retention within the lagoon imposed by its restricted water connection to the sea.