The unexpected climate changes are causing rainfalls to exceed the design frequency, which complicates the management and operation of agricultural reservoirs and increases the risk of overflow. According to the “Planning and Design Standards for Agricultural Prediction Infrastructure Maintenance Project (Fill Dam Section),” agricultural reservoirs were originally designed without flood control functions, with the standard being to directly discharge incoming flood. Based on this foundation, this study assesses the overflow risk of agricultural reservoirs using the concepts of inflow and outflow theories as well as storage capacity. The balance when inflow and outflow are at their maximum was analyzed for prioritized areas, focusing on the flood management area (the area between the full water level and crest elevation) relative to the basin area, to examine the feasibility of balance through flood routing. The proposed method is easily accessible to facility managers, enabling them to assess the risk of reservoirs for efficient management and operation during floods.