© 2020 John Wiley & Sons Ltd Carbon isotopes (δ13Corg) in biomass, carbon (δ13Ccarb) and oxygen (δ18Ocarb) isotopes in authigenic calcite and estimations of chemical weathering of siliciclastic minerals (chemical index of alteration [CIA] and plagioclase index of alteration [PIA]) in lacustrine sediments of the ephemeral Babicora Basin, located within the core region of the North American Monsoon at northwest Mexico, helped to evaluate the source of biomass, variations in hydrological balance and sediment–water interactions during three different marine isotope stages (late MIS 4: ≥65.4–59.5 cal ka BP, MIS 3: ~59.5–28 cal ka BP and MIS 2: ~28–15 cal ka BP) of the last glacial. Comparisons of δ13Corg with previously published records of C/N, diatom abundance and fossil pollen indicate that biomass of the late MIS 4 was sourced from C3 aquatic and land plants. During the MIS 3, the C3 plants continued to contribute biomass and the influence of lacustrine algae, however, increased during its later part. The water column experienced more evaporation compared to two other MIS stages and sediment–water interactions varied between minimal to moderate (CIA: 49–68). Sediments were transported for longer distances during the wetter intervals and eroded from nearby lithologies during the drier intervals. Interactions between sediments and inflowing water (CIA: 59–65) remained homogeneous during the MIS 2. Source of the biomass, however, was variable. Lacustrine algae and C3 land plants contributed biomass during the early MIS 2 (~28–19 cal ka BP) and contributions from the C4 and CAM vegetation slightly increased towards the deglaciation (~19–15 cal ka BP).