An investigation of the water quality in an under-populated watershed was conducted over a 15-year period in which data was collected at weekly intervals. The purposes of this study were to analyze the long-term trends in water quality and to evaluate the relationship between the water quality and precipitation. Concentrations of total phosphorus (T-P), chemical oxygen demand (COD), and suspended solids (SS) reached remarkably high values under heavy precipitation conditions, and these concentrations increased exponentially with the amount of precipitation. Over the course of this study, the population, number of factories, animals (cow and pig), and area of agricultural land exhibited clearly decreasing trends, while steady progress in domestic wastewater treatment was realized. However, no clear decrease in the parameters of water quality was observed, and some nitrogen, phosphorus, and COD concentrations increased even though no significant change in precipitation occurred. A possible hypothesis explaining this lack of a clear decrease in water quality is that specific pollutant outflows from forests and agricultural lands may have increased in recent years. This is because poorly managed forests and agricultural lands in the under-populated watershed have adversely affected the water quality of the rivers.