In this research paper, a flash flood modeling system implemented in a Mediterranean river basin is presented. Radar precipitation estimation along with hydrological modeling techniques are implemented within the system for simulating the runoff generation and routing processes occurring in the catchment. However, there exists an uncertainty related with the estimation of radar precipitation (Zawadzki, 1984) and from model calibration (Beven, 2006). Such uncertainty is propagated to the resulting discharge simulations. The aim of this research paper is to propose a methodology to analyze the propagation of uncertainty occurring at the different processes of the modeling system. For this purpose, a Monte Carlo simulation approach is used to consider the uncertainty arising from rainfall and model parameter estimation.