Analysis of sediment cores from organic lakes in central Yukon Territory, Canada suggest changes in Holocene sediment delivery mechanisms occurred as mode shifts, rather then gradational changes. There appear to have been two alternating depositional modes during the Holocene, which are mirrored to varying degrees by other proxy data. Grain size, macrofossil, LOI organic carbon and magnetic susceptibility (MS) analyses demonstrate a warm, stable early Holocene characterized by fine-grained sediments, high LOI, low MS and warm water macrophyte species. Climate began to cool at ca. 7500 BP, followed by a major shift in sedimentary environment at ca. 4000 BP. This change is reflected in grain size, LOI, MS and macrofossil assemblage, suggesting it represents a major change in climate, possibly correlative to the beginning of the neoglacial. Warmer conditions returned between ca. 1500 and 500 BP. with finer grain sizes, increased organic carbon and the reappearance of warm water macrophytes. Climate after 500 BP appears to have cooled, with coarser, more well sorted grain size distributions, lower LOI and higher MS. This study demonstrates the utility of grain size analysis as a paleoenvironmental proxy indicator, and reveals a more dynamic Holocene climate in central Yukon Territory than previously thought.