Lake sediment cores were collected from the Rwenzori Mountains, Uganda-Democratic Republic of Congo from three lakes: Lake Kopello (4,017 m asl), Lake Africa (3,895 m asl), and Lake Mahoma (2,990 m asl). Analysis of the recovered cores focused on the late Pleistocene and Holocene at centennial resolution. Sediments were prepared for biomarker analysis, and we report leaf wax δ2Hprecip and δ13Cwax. These data provide the montane climate and vegetation history of the Rwenzori Mountains at varying elevations.