The degree to which different lakes within a landscape respond coherently (in unison) to external drivers such as climate change and soil development is uncertain. Presentation of multi-proxy, geochemical and palaeoecological data from individual lakes in the form of fluxes minimizes distortions resulting from variable sedimentation rates and changes in sediment composition. We use the accumulation rates of magnetic minerals, total organic C and N, terrestrial and aquatic biomarkers, graminoid epidermis, pollen, green algae, diatoms and diatom C in four small lakes, situated between 2350 and 4595 m a.s.l. on the NE flank of Mt. Kenya, East Africa, to reconstruct changes in C cycling over the last 38 ka. The results conflict with earlier models of landscape and lake development, showing: (1) that glacial–interglacial changes in vegetation cannot be interpreted as simple, altitudinal shifts in the modern vegetation belts; and (2) that limnological changes were not coherent. Rapid variations in climate, water level, erosion and nutrient input overwhelmed long-term, successional trends in lake sedimentation and C accumulation since the Last Glacial Maximum. The results also reveal previously unrecognized features of the palaeoenvironmental record, such as the rapid degradation of organic matter in diatoms and the occurrence of a productive, fire-prone montane grassland during the highly seasonal, monsoonal climate of the Lateglacial and early Holocene.