A small dam is of hydraulic structures, which is always exposed to risk by flood, and it’s very important to ensure structural safety. A probabilistic analysis, quantifying variable as a risk factor to ensure safety of small dam, identifying its coefficient of variation, which has become increasingly important. In this study, the risk of seepage failure of foundation within a small dam was estimated based on flood scenarios by rainfall quantile. The final compound risk was evaluated combining probabilities, related to seepage failure and flood level. The seepage failure probability was estimated by performing seepage analysis depending on the water level difference between upstream and downstream in small dam. The probable flood level was estimated by considering hydraulic uncertainty associated with channel geometry, and movable gate operation during the flooding season, applied a probable flood considering hydrologic uncertainty evaluated by Bayesian approach. The safety evaluation of small dam with probabilistic-based compound risk expect to use the index for hydraulic structure design in the future.