We present varve chronologies for sediments from two maar lakes in the Valle de Santiago region (Central Mexico): Hoya La Alberca (AD 1852–1973) and Hoya Rincón de Parangueo (AD 1839–1943). These are the first varve chronologies for Mexican lakes. The varved sections were anchored with tephras from Colima (1913) and Paricutín (1943/1944) and 210Pb ages. We compare the sequences using the thickness of seasonal laminae and element counts (Al, Si, S, Cl, K, Ti, Mn, Fe, and Sr) determined by micro X-ray fluorescence spectrometry. The formation of the varve sublaminae is attributed to the strongly seasonal climate regime. Limited rainfall and high evaporation rates in winter and spring induce precipitation of carbonates (high Ca, Sr) enriched in 13C and 18O, whereas rainfall in summer increases organic and clastic input (plagioclase, quartz) with high counts of lithogenic elements (K, Al, Ti, and Si). Eolian input of Ti occurs also in the dry season. Moving correlations (5-yr windows) of the Ca and Ti counts show similar development in both sequences until the 1930s. Positive correlations indicate mixing of allochthonous Ti and autochthonous Ca, while negative correlations indicate their separation in sublaminae. Negative excursions in the correlations correspond with historic and reconstructed droughts, El Niño events, and positive SST anomalies. Based on our data, droughts (3–7 year duration) were severe and centred around the following years: the early 1850s, 1865, 1880, 1895, 1905, 1915 and the late 1920s with continuation into the 1930s. The latter dry period brought both lake systems into a critical state making them susceptible to further drying. Groundwater overexploitation due to the expansion of irrigation agriculture in the region after 1940 induced the transition from calcite to aragonite precipitation in Alberca and halite infiltration in Rincón. The proxy data indicate a faster response to increased evaporation for Rincón, the lake with the larger maar dimensions, solar radiation receipt and higher conductivity, whereas the smaller, steeper Alberca maar responded rapidly to increased precipitation.