Previous studies have shown that moisture availability in the central highlands of Mexico during the last 3000 years has been highly variable, but evidence remains ambiguous since the climatic signal is partially masked by that of human activity. Here we use two isotope systems to provide evidence for environmental change in Laguna Zacapu, Michoacán covering this time period. Carbon isotope ratios of organic material suggest that there have been fluctuations in the carbon pool related to plant productivity, possibly as a result of changes in the abundance of aquatic plants around the lake margins. The drainage basin and lake have been managed intensively during the 20th century. Lake level apparently fell during the early part of the century, but has been artificially controlled since the 1950s. The oxygen isotope ratios from diatom silica should provide the more unambiguous climate signal, although we show that the interpretation of the diatom oxygen isotope record is far from straight forward. Zacapu is a spring-fed, non-evaporating system and changes in δ18Odiatom are likely to be a function of changes in δ18O of precipitation, due to either temperature and salinity variation in the Gulf of Mexico (associated with changes in the Bond cycles from the North Atlantic or the Loop current from the Carribean) and/or changing moisture contributions from different air masses (Gulf of Mexico vs. Pacific). Changes in the Gulf of Mexico are possibly at a resolution comparable to the periodicity we see in the δ18Odiatom record, although without better dating the comparison is speculative.