A 292-cm-long sediment core was collected from the center of Yukashigata Lagoon using a Mackereth air-pressure piston corer. Pollen analysis with radiocarbon dating of this sediment core was conducted to reconstruct the surrounding paleoenvironment. The results revealed a decrease in evergreen broadleaf tree pollen grains, an increase in herb pollen grains and fern spores, and a slight increase in charcoal fragments around 1100 cal CE, suggesting the onset of human impact on vegetation around this time. A major vegetation shift occurred around 1300 cal CE, marked by a rapid increase in Pinus pollen grains, herb pollen grains, and fern spores, along with a decrease in evergreen broadleaf tree pollen grains. The latter change suggested large-scale destruction of vegetation. Subsequently, tree pollen grains continued to decline, with a further decrease around 1550 cal CE, perhaps caused by the extensive use of Kumano timber for the construction of castles and temples by Sengoku-period warlords. Much of this timber was supplied by the Kishu Domain. However, as the Kishu supply of high-quality timber began to deplete, the warlords shifted to a policy of forest protection and cultivation, banning the felling of six tree species. As a result, the abundance of Pinus and Cryptomeria pollen grains sharply increased from around 1650 cal CE, as did that of evergreen broadleaf tree pollen grains which indicated a transition from compensatory vegetation to evergreen broadleaf forest from around 1950 cal CE. This vegetation recovery appears to have been linked to increasing reliance on plant-based fuels as fossil fuels became more widely adopted.