The actual conditions of groundwater use in an irrigated paddy area in the Echi River alluvial fan with multiple water resources were clarified to evaluate influencing factors of groundwater use and to consider how to establish its sustainable use. Groundwater is managed by two kinds of organizations, the land improvement district that has the responsibility for sending irrigation water to the entire command area through principal distributing systems, and the farmers or the water users associations that irrigates paddy plots in the terminal command areas controlling terminal division works and groundwater pumping wells. Groundwater use in the entire command area compensates for the shortage of surface water intake and complements the fluctuation of surface water intake due to meteorological conditions. Water managers use groundwater with excellent handleability responding to the changes in precipitation and situation of rice growth stages in the terminal plots. The appropriate division of roles and cooperative works among the two different organizations are important for desirable agricultural groundwater management.