Annual and daily runoffs at most locations of a basin are unknown, which are estimated by the proposed methodology. First a squared region covering the Fuji River basin is divided into 9, 450 grids of nearly 1 km². Annual or daily precipitation data of 27 gauges in the region are used to derive the precipitation at each grid, by applying a spatial interpolation algorithm called spline function. Monthly ordaily mean temperatures at grids are estimated by a step-wise regression method. Second annual water yield at any grid is obtained with Hamon and Pike formulas and the water budget equation. Runoff distribution in the river network drawn out using digital elevation data is estimated. Finally, based on daily rainfall and temperature, the daily runoffs along the rivers are simulated by a distributed hydrologic model. All runoff estimations are checked by the observations in several sites.