The research presented in this thesis addresses the uncertainty in flood inundation modeling, which may arise from input data and hydraulic modeling approach. The study area is the Sungai Johor basin in Johor, Malaysia, an agriculture-dominated area. The present study analyses the modelling uncertainties arising from estimations of design flow, terrain data sets, geometric description in hydraulic models and different modeling approaches, and develops recommendations for practitioners. Explicit account for uncertainties and studying their impact in flood inundation mapping allow for more informed and effective decision making.