Stable isotope altimetry is a useful tool for estimating paleoelevation in sedimentary records. Yet questions remain regarding how source moisture, climate, and local topography can influence these estimates. Here we present stable isotope altimetry results on late Quaternary pedogenic carbonates of known elevation on both flanks of the Andean orogen at 33°S. We measured δ18O values of pedogenic carbonates and river water samples from small drainages at regular elevation increments within the Río Aconcagua (Chile) and Río Mendoza (Argentina) catchments. The δ18O values of river waters correlate well with elevation and show similar isotopic gradients between the Chilean (−3.7‰/km) and Argentine (−4.8‰/km) sides of the range. Uncertainties associated with scatter in the river water data and assumptions about the temperature of carbonate formation indicate that elevation estimates have 1σ errors of 350–450 m. We estimate the isotopic composition of soil water from pedogenic carbonates on both sides of the range by assuming mean annual temperatures based the modern temperature lapse rate from meteorological station data. Combined, our data show that stable isotope altimetry produces reasonable estimates of modern elevation, with the majority of our samples (60%) within the 1σ uncertainties and 77% within 2σ.