The recognition of vegetation changes induced by volcanic eruption is particularly important for paleoenvironmental studies in volcanic regions. In this study, we examined the molecular and stable carbon isotopic compositions (δ13C) of sedimentary leaf wax n-alkanoic acids from Lake Yamanaka at the northeastern foot of Mt. Fuji, central Japan, to distinguish volcanic effects on biomarker δ13C proxies from other environmental influences over the past 15,000 years. The δ13C values of C30 acids showed a significant positive correlation with average chain length (ACL24–30), suggesting that δ13C reflects plant physiological responses to changes in water availability for C3 plants. The δ13C values of C30 acids showed patterns similar to those of Holocene stalagmite δ18O records in Chinese caves, indicating that variations in hydroclimate at the northeastern foot of Mt. Fuji are controlled by large-scale changes in Asian monsoon activity. In contrast, the δ13C values of C24–C28 acids increased abruptly at ca. 1750 and 1100 cal yr BP, which coincide with eruptive events at the northeastern flank of Mt. Fuji. This suggests an increase in input from C4 plants, likely reflecting an increase in C4Miscanthus grass, a pioneer species on volcanic deposits, following by the devastation of forest by the eruptions.