This study presents a risk analysis model to evaluate the failure risk for the flood-control structures in the Keelung River due to the uncertainties in the hydrological and hydraulic analysis, including hydrologic, hydraulic, and geomorphologic uncertainty factors. This study defines failure risk as the overtopping probability of the maximum water level exceeding the levee crown, and the proposed risk analysis model integrates with the advanced first-order and second-moment (AFOSM) method to calculate the overtopping probability of levee system. The proposed model is used to evaluate the effects of the freeboard and flood-diversion channel on the flood-control ability of the levees in the Keelung River, which were designed based on the 3-day, 200-year design rainfall event. The numerical experiments indicate that the hydrologic uncertainty factors have more effect on the estimated maximum water level than hydraulic and geomorphologic uncertainty factors. In addition, the freeboard and the flood-diversion channel can effectively reduce the overtopping probability so as to significantly enhance the flood-control capacity of the levee system in the Keelung River. Eventually, the proposed risk analysis successfully quantifies the overtopping risk of the levee system under a scenario, the increase in the average 200-year rainfall amount due to climate change, and the results could be useful when planning to upgrade the existing levee system.