The first paleoecological reconstruction of the biogeochemical conditions of the Gulf of Batabanó, Caribbean Sea was performed from (210)Pb-dated sediment cores. Depth profiles of 20 major elements and trace metals, organic compounds, grain size, and mollusk assemblage composition were determined from 9 stations encompassing unconsolidated sediments in the gulf. Spatial heterogeneity was evident for the geochemistry of sediments and for the mollusk assemblage composition. Our reconstruction indicates that pollution is not a critical threat to the ecosystem, although a slight historical increase of lead enrichment factor was detected probably due to long-range atmospheric fallout. Mollusk assemblages were composed by 168 species belonging to 59 families and no temporal trends in the species diversity or assemblage composition were detected, suggesting no depletion of diversity or habitat loss. Other signals of habitat loss such as changes in organic budget or increase of fine sediment fraction were absent or weak. Nitrogen retained in sediments changed by <1% in the century, indicating no historical events of eutrophication or oligotrophication in the gulf. Historical decrease of fine sediment fraction in the eastern sector would be linked to modifications in sedimentation rate, land use, and/or particle transport from the shelf border; this also suggests that both sectors have different sedimentary dynamics. Although, on theoretical grounds, historical fishery may have caused deleterious ecosystem effects by overexploitation of spiny lobster stocks, no evidence of habitat degradation or loss, caused by fisheries, could be detected.