This dataset comprises multiproxy biogeochemical (elemental and isotope geochemistry, visible-near infrared spectroscopy, computed tomography, magnetic susceptibility) data and diatom assemblage data for sediment sequences retrieved from lakes Santa Maria del Oro (Nayarit, Mexico) and Teremendo (Michoacán, Mexico) in April 2022. The data cover a time period from 2022 to around 1650 and were used to explore connections between lake carbon cycling and related ecosystem processes under natural and anthropogenic environmental change over the past four centuries.