The sensitivity of East Africa’s environment to anthropogenic and natural climatic changes is poorly understood. Therefore, there is need to incorporate continuous high-resolution records to provide insights into the timings of climatic signals to reconstruct East Africa’s paleoenvironment. This study presents sediment core data (KAP-01) from Kapkanyar Swamp, Cherangani Hills, based on fungal spores, Loss-On-Ignition (LOI) and microscopic charcoal analyses. The climate during the Last Glacial Maximum (LGM) was generally cold and dry with intermittent presence of moist environmental conditions evidenced by the minimal presence of coprophilous taxa, a well-known taxon used to signify presence herbivores, representing diminished fauna. Presence of charcoal in the LGM reflects probable natural fires suggesting dry environmental conditions. The deglaciation period, on the other hand, was relatively colder and drier compared to any other period in the last ~23 Kyrs with scanty preservation fungal spores. The Holocene period is characterized by increased fungal assemblages, indicative of a moist environment punctuated by drought episodes evidenced by fires and fungal spores such as Tetraploa, Meliola, and Glomus. In the Late Holocene, fires are more frequent and with potential fire breaks suggesting anthropogenic controlled fires. Our results depict anthropogenic imprints in the environment in the Late Holocene period, ~4 Kyrs to the present.