Differential sources of sedimentary organic compounds in a volcanic region were revealed by determining radiocarbon content (Δ14C) of organic compounds in surface sediments from Lake Kawaguchi, at the northern foot of Mount Fuji, central Japan. The Δ14C values of C16 fatty acid (−124‰) and chlorophyll a (Chl a) (−133‰) were similar to the Δ14C of dissolved inorganic carbon (DIC) in surface water (−117‰), suggesting that a significant portion of these compounds originated from modern primary producers with a reservoir age of ~1000 years. On the other hand, a large offset between the Δ14C values of Chl a (−133‰) and those of 132, 173-cyclopheophorbide-a-enol (−169‰) and pheophytin a (−179‰) suggested contributions from older pigments. In addition, the Δ14C of long-chain (C24, C26, and C28) fatty acids (−183 to −75‰) showed a large offset from that of a plant leaf remain (0‰) within sediments, demonstrating that the long-chain fatty acids were affected by substantial contributions from pre-aged terrestrial materials. Overall, the sedimentary organic compounds gave 14C ages older than the plant leaf fragment within sediments; however, the similarity between Δ14C of the C16 fatty acid and DIC implies potential for applying compound-specific radiocarbon analysis as a dating tool in volcanic lake environments.