We present a record of climate variability spanning the last 2000 years obtained from sediment cores retrieved south and west of Puerto Rico in the northeastern Caribbean Sea. The records include lithological and mineral magnetic parameters as well as planktonic foraminifer data. For chronostratigraphic control, AMS 14C and 210Pb/137Cs measurements were made. Harmonic analysis of the values of the mineral magnetic parameters “saturation isothermal remanent magnetization” (SIRM), “anhysteric remanent magnetization divided by magnetic susceptibility” (ARM/χ), and “saturation isothermal remanent magnetization divided by magnetic susceptibility” (SIRM/χ) indicate the existence of a ∼200-year-long climate cycle in the northeastern Caribbean during the last 2000 years. The detected cycle may reflect changes in precipitation patterns over the low-latitude North Atlantic Ocean and surrounding continental areas. Higher organic carbon contents appear in the sediments both off southern and western Puerto Rico before and at the onset of the Little Ice Age around A.D. 1300 to 1500. This is indicative of increased run off and/or enhanced surface productivity possibly associated with more intense wind-induced upwelling. Major changes in the geochemical and mineral magnetic records around A.D. 850–1000 concur with changes in other records from the Caribbean and North African regions indicating a shift toward a more humid climate over the low-latitude North Atlantic.