A probabilistic risk analysis of levee system estimates the overall level of flood risk associated with the levee system, according to a series of possible flood scenarios. It requires the uncertainty analysis of all the risk components, including hydrological, hydraulic and geotechnical parts computed by employing MCMC (Markov Chain Monte Carlo), MCS (Monte Carlo Simulation) and FOSM (First- Order Second Moment), presents a joint probability combined each probability. The methodology was applied to a 12.5 km reach from upstream to downstream of the Gangjeong-Goryeong weir, including 6 levee reaches, in Nakdong river. Overtopping risks were estimated by computing flood stage corresponding to 100/200 year high quantile (97.5%) design flood causing levee overflow. Geotechnical risks were evaluated by considering seepage, slope stability, and rapid drawdown along the levee reach without overflow. A probability-based compound risk will contribute to rising effect of safety and economic aspects for levee design, then expect to use the index for riverside structure design in the future.