Lakes bury significant amounts of organic carbon (OC) in their sediments contributing to the removal of carbon from the short-term carbon cycle. Mounting evidence points to broadscale increases in lake OC burial rates under growing human perturbation; however, the extent and mechanisms giving rise to this trend are not well understood in the context of tropical regions. We sought to expand knowledge of natural and anthropogenic controls of lake carbon cycling at lower latitudes by investigating four centuries of changes in the carbon sink of two tropical lakes in Central Mexico. Multiple biogeochemical and paleoecological indices were used to track temporal trends in OC production, inflow and burial, and to identify underlying environmental drivers. We uncovered systematic patterns in lake carbon dynamics in both studied lakes, including a three- to seven-fold increase in OC burial over recent decades. Marked increases in OC production over the 1900s in both lakes may have contributed to the enhanced carbon sink. However, increased sediment accumulation rates, particularly over the past couple of decades, suggest that the predominant factor influencing increased OC burial rates was related to growing local human disturbance. Over the last four centuries, sediment biogeochemistry in both lakes suggested shifts in water balance and lake levels that appear to be important drivers of OC production and organic enrichment in the lakes, linking them to regional climate variability.