Developing a floodplain map often requires flood inundation modeling. A common representation of simulated results is based on deterministic approaches, where a single outcome is produced without an explicit consideration of the uncertainties in the modeling process. The research presented in this thesis deals with uncertainty in flood inundation modeling caused by input data and hydraulic modeling approach. The study area is the Sungai Johor basin in Johor, Malaysia. The case study shows the uncertainties arising from the estimation of design flow, terrain data sets, geometric description in hydraulic models and modeling approaches.