The purpose of this research is to understand the change of runoff characteristics by estimated spatial rainfall. Therefore, this paper largely composed of two parts. First, we compared the simulated result according to estimation method, ID(Inverse Distance Method, ID2(Inverse Square Distance Method), and Kr(General Covariance Kriging Method), after letting miss rainfall data to the observed data. Second, we reviewed the runoff characteristics of the distributed runoff model according to the estimated spatial rainfall. On the basis of Yuseong water level station, we select the target basin as Gabchun watershed. We assumed 1 point or 2 point of the 6 rainfall gauge stations in watershed were missed. We applied the spatial rainfall distributed by Kr to Hy-GIS GRM, distributed runoff model. When 1 point rainfall data is missed, Kr is superior to others in point rainfall estimation and runoff estimation of Hy-GIS GRM. However, in case rainfall data of 2 points is missed, all of three methods did not give suitable result for them. In conclusion, Kr showed better applicability than other estimated methods if rainfall’s data less than 2 points is missed.