Land use and land cover changes (LULCC) are a global environmental issue that has impacted biogeochemical cycles worldwide. Sedimentary records can demonstrate the effects of LULCC on aquatic ecosystems, where the recent urbanization has been linked to changes in carbon and nitrogen burial. In this study, we reconstructed long-term LULCC and sedimentary records of carbon (C), nitrogen (N), phosphorus (P), and sediment burial rates in a eutrophic tropical coastal lagoon affected by recent urban expansion. Based on analyses of 30 years of satellite imagery and sedimentary records from 1932 to 2013, we revealed that urban expansion over low-productivity agricultural-pasture areas increased siltation and C, N, P concentrations and fluxes in the coastal lagoon. Large temporal variability of such parameters revealed not only the effects of LULCC on the lagoon's burial rates, but also the influence of artificial sand barrier openings, which connect the studied lagoon to the sea, reducing C, N, P, and particle deposition in the sediment. Our results support multi-proxy methods to assess the relationships between recent urbanization, rising C, N, and P burial rates, and the eutrophication process. We highlight that artificial sandbar openings, the current eutrophication management strategy for coastal lagoons, are ineffective in reducing the eutrophication state, even in the recent scenario of decreasing C, N, and P burial rates.