In Central America and the Caribbean, periods of increased aridity that correspond to the Terminal Classic Drought (TCD; 1200–850 cal yr BP) and the Little Ice Age (LIA; 500–100 cal yr BP) have been documented in many paleoclimate records. Compound-specific hydrogen (δDalkane) and carbon (δ13Calkane) isotopic compositions of n-alkanes in lake sediment can be used to interpret changes in paleoprecipitation and terrestrial paleovegetation, respectively. To assess the climate forcing mechanisms that drove the TCD and LIA, we established a multidecadal to centennial-scale late-Holocene reconstruction of precipitation variability and vegetation change at mid-elevation on the Caribbean slope of Costa Rica, developed from new δDalkane, δ13Calkane, and geochemical analyses and previous pollen and microscopic charcoal analyses from a sediment core from Laguna María Aguilar. Laguna María Aguilar is a freshwater lake located at 770 m elevation on the Caribbean slope of the Cordillera Central. During the TCD, δDalkane data for María Aguilar indicate relatively wet conditions compared to the mean δDalkane value for the entire record. Other proxy records for the TCD indicate that the Pacific slope of Costa Rica and sites above 3400 m near the continental divide experienced generally drier conditions than mid- and low-elevations on the Caribbean slope. We conclude that the TCD may have been driven by both Pacific and Atlantic climate-forcing mechanisms. During the LIA, the Laguna María Aguilar δDalkane record indicates an increase in hydroclimate variability, with some of the highest recorded δDalkane values (driest conditions) during the earliest portions of the LIA, but conditions were not persistently dry for the entirety of the LIA. Based on regional paleoclimate records overall, the LIA drought appears to be more clearly expressed on the Caribbean slope than on the Pacific slope of Costa Rica, indicating that the LIA was perhaps driven primarily by Atlantic Ocean conditions and climate dynamics.