The Lake Biwa–Yodo River Basin, with a catchment area of 8,240 km², is vital for Japan's water resources. Located upstream, Lake Biwa is Japan’s largest freshwater lake and the third oldest in the world. It supplies water to approximately 14 million people, supporting drinking water, industry, agriculture, and hydroelectric power. Although Shiga Prefecture implemented various measures to control water pollution during Japan’s rapid economic growth, the chemical oxygen demand (COD) of Lake Biwa began increasing around the mid-1980s. Several studies have suggested that the accumulation of non-biodegradable dissolved organic matter (NBDOM) contributed to this trend. To investigate the potential causes, historical water quality and statistical data were analyzed. It was hypothesized that the decline in forestry workers led to the degradation of coniferous plantation forests, resulting in the loss of understory vegetation and the expansion of bare land, which may have partially contributed to the rise in COD. Forest degradation seems to enhance soil erosion and alter soil organic matter quality, thereby increasing the loading of NBDOM into Lake Biwa. The objective of this research was to evaluate the biodegradability of water-extracted organic matter (WEOM) from the soil in a degraded forest. A surface soil sample was collected from a coniferous plantation forest, which has been abandoned for several decades, within the Suntory Natural Water Sanctuary agreement area. For comparison, another surface soil sample was also collected from a managed forest in the same mountain area. The soil samples were air-dried, sieved, and subjected to water extraction at a 10:1 water-to-soil ratio, followed by membrane filtration. The WEOM was diluted and used for a 14-day biodegradability test under dark, aerobic conditions at 25 °C. Dissolved organic carbon (DOC) concentration, ultraviolet absorbance, and three-dimensional excitation-emission matrix fluorescence spectra were measured before and after the test. The initial DOC concentrations were 68.3 mgC/L for the degraded forest and 52.5 mgC/L for the managed forest. The DOC-based biodegradability was 13.7% for the degraded forest and 31.9% for the managed forest. The input loading potential of NBDOM per unit mass of dry soil in the degraded forest was approximately 1.7 times higher than that from the managed forest. It is indicated that forest abandonment and degradation increase NBDOM influx into Lake Biwa. Considering that climate change may alter precipitation patterns and further enhance soil erosion, the actual influx of NBDOM into Lake Biwa and downstream could be even greater than estimated in this research.