To determine the appropriate long-term rainfall index for warning and evacuation from debris disaster, runoff monitoring of multi-scale nested catchments (headwater streams, 4 to 6 km2 catchments, and a 70 km2 catchment) have been conducted in the upstream of Kamanashi River, central Japan. Using stream discharge peak and recession curve, the relationship among basin scale, underlying geology and runoff response were evaluated. The suitable long-term rainfall index was determined by comparing stream recession curve and the effective rainfall with different half life period. The recession analysis of stream flow revealed that stream recession insensitive to catchment size but controlled by underlying geology. The half-life time of the estimated effective rainfall was 48 hours in granite, 72 hours in a sedimentary rock, 168 hours in limestone. The estimated half life period using the area ratio of catchment geology also show good agreement to the actual recession data. These finding suggest that runoff monitoring for square km scale is encouraged, and determining appropriate half life of each geology is important for future warning and evacuation plan.