This study aimed to assess factors that determine changes in river water level in a relatively large forested catchment. Analysis of official river flow data for the Aya-minami River in Miyazaki, Japan, revealed a significant reduction for several years after 1970 and a prolonged reduction over 36 years in 95-day flow, 185-day flow, and 275-day flow; the climatic factors and changes in water use during this period had not contributed to this reduction. Forests cover approximately 90% of the 5,884 ha catchment area, and an analysis of tree ages showed that the clear-cut in the 1960s and 1970s most probably resulted in an elevated flow level around 1970, and that the tree growth thereafter have reduced discharges from the forest area. No statistically significant reduction trend was observed in the 355-day flow. Discharges from broad-leaved forests during periods of less precipitation tended to be higher than that of coniferous forests in small catchments, though we could not confirm that larger discharges from broad-leaved forests replenish the 355-day flow of the Aya-minami River.