Flooding one of the problems that arise during the rainy season. This is very common in areas with tropical climates, where during the dry season it can be very dry and lack of water, but during the rainy season it is abundant with water and at worst a disaster can occur. Runoff and inundation a usually problem in Jayapura City, with hill topography that tends the large, resulting flood and inundation in flat and upstream areas. One the public areas is often affected by runoff or flood and innudation at the SMA 4 area of Jayapura City, where in this area is most important community activity because it is related to educational activities so attention need paid overcome the problems that occur mainly as a result of runoff. Sustainable drainage system application that prioritizes water quality and runoff water quantity management is very important to overcome the problems runoff and innudation. The result study is find a solution to runoff and iinudation. Analysis method useing Hec-Ras application for calculation discharge and channel dimensions using Sustainable Urban Drainage method which is popularly applied in various countries for water quality and runoff quantity management. The researched result are to obtain the maximum rainfall discharge value and runoff design, drainage channel dimensions, and the appropriate sustainable drainage system in SMA 4 area of Jayapura City[1].