Coastal lagoons are very sensitive to anthropogenic impacts and sedimentary records may provide valuable temporal reconstructions of the environmental changes in the lagoon, the coastal zone, and the catchment area. The Alvarado Lagoon (Veracruz, southwestern gulf of Mexico) belongs to an extensive complex of wetlands recognized as a Ramsar site. However, its catchment basin has one of the highest deforestation rates in Mexico due to the transformation of lowlands for agriculture and grazing, thus causing siltation of the surrounding aquatic bodies. To evaluate the impact of land use change on Alvarado Lagoon, sediment fluxes and provenance were reconstructed by studying the elemental composition (determined by X-ray fluorescence spectrometry) of a sediment core dated radiometrically (210Pb, 137Cs, 239,240Pu). The sedimentary record showed an acceleration of the sediment accumulation rate during more than 134 ± 17 years; however, the changes in elemental composition during the past 40 years (i.e., 1972–2011) indicated the incorporation of continental weathered sediments and an increment of sediment accumulation of circa 470%, in coincidence with the period of higher deforestation and siltation. The recent increase in sediment accumulation rates and changes in geochemical features are attributed to erosion caused by land use changes in the Alvarado Lagoon drainage basin.