Due to the presence of various uncertainties, in additional to hydrologic inherent randomness, the performance reliability associated with hydraulic infrastructure is less than the anticipated reliability for a specified hydrologic return-period used in determining flood protection capability. Climatic change in the foreseeable future might have altered hydro-meteorological environments in Taiwan and introduce more complexity and uncertainty in hydrological and hydraulic characteristics in hydrosystem infrastructural designs. For the safety of hydraulic infrastructures, excluding reservoirs, this study attempts to identify and evaluate the uncertainty factors in hydrological and hydraulic analysis in the design of hydraulic infrastructures. Furthermore, the study develops a risk analysis procedure which can be used for establishing flood protection and mitigation schemes and strategies. In the study, uncertainty factors are categorized into hydrologic factors (rainfall amount, pattern, and coefficients of the rainfall-runoff model), hydraulic factors (boundary condition of water level, weir coefficients of the flood-diversion channel, and roughness coefficients) and geomorphologic factors (land-use, erosion and siltation of river beds). Based on the above uncertainty factors, the risk analysis procedure and model are developed to evaluate overtopping probability of levee systems and to perform reliability assessment for of hydraulic infrastructures. For demonstration purpose, the flood control system along the Keelung River is chosen as the case study. From the numerical experiments, the proposed framework can be applied to risk assessment of the flood protection capacity of hydraulic infrastructures resulting from uncertainty factors in the hydrological and hydraulic analysis.