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We compared the stratigraphy of sediment cores that span the last 13,000 yrs from three sites in the main basin of Lake Titicaca, Boliva/Peru as indicators of regional paleoclimate. The cores show similar patterns of change after ~6,400 calendar yrs before present (cal yr BP) but differ before that time. Site NE98-PC2, which is near the Rio Illave and its delta, shows differences in diatom species composition and in calcium carbonate concentrations relative to cores from the other two sites, particularly during times of inferred high precipitation. In contrast, the carbon isotopic stratigraphy of the three sites is relatively similar. The magnetic susceptibility data suggest that the proximity of site NE98-PC2 to the river and delta resulted in higher loads of detrital sediment prior to 6,400 yr BP, whereas pelagic sources contributed most of the sediment at the other sites. These differences highlight the potential for spatial heterogeneity of sediment records in large lake systems and the importance of evaluating multiple cores for robust interpretation of paleoenvironmental history.