More than 60% of river runoff from the Lena River basin originates in the southern mountainous region of eastern Siberia within the permafrost zone. We studied the transport of dissolved organic carbon (DOC) and particulate organic carbon (POC) within the Mogot Experimental Watershed, which is close to the drainage divide between the Lena and Amur River basins in the southern mountainous taiga region, from 1 August 2000 to 12 November 2001. DOC concentration was strongly related to thawing depth at the bottom of the main valley when thawing depth was less than 20 cm during snowmelt runoff. When thawing depth was equal to or greater than 20 cm, DOC concentration was more closely related to the rate of river discharge in summer runoff. On the basis of our observations, we extrapolated the annual transport of DOC and POC to be 4.75 g C m−2 yr−1 and 0.03 C kg C m−2 yr−1, respectively. Transport of organic carbon from the catchment was about 4.78 g C m−2 yr−1 during 2001. DOC is the main form of organic carbon flux in the study area.