We analyzed the δ2H composition of n-alkanes isolated from Laguna Zoncho, a small lake in southern Pacific Costa Rica, to reconstruct paleohydrology. Using a core that spans the past 3600 years, we found evidence of dry periods, most notably during the Terminal Classic Drought (TCD; ~1200 cal yr BP) and the Little Ice Age (~400 cal yr BP). Previous work at Laguna Zoncho, using bulk sedimentary δ13C and geochemical analysis, found that agriculture began to decline during the TCD. Our δ2H records confirm the occurrence of arid conditions coincident with the TCD at Laguna Zoncho and show that, despite receiving more than 3000 mm of precipitation per year, this region is susceptible to multidecadal droughts.