Abstract: This study presented a flood estimation model for Johor River in Kota Tinggi watershed, Malaysia using HEC-HMS (Hydrologic Modeling System). Calibration and validation processes were carried out using different sets of data. Evaluation on the performance of the developed flood model derived using HEC-HMS yield a correlation coefficient R2 close to 1. The simulated Qpeak are 150.9 m3 sec-1, while the observed Qpeak for 10 years record (1997-2006) is 145.12 m3 sec-1. The percentage of error values are 4% and the performance of the developed flood model derived using the HEC-HMS with R2 value is 0.905. Based on these findings, it is suggested that the developed model using HEC-HMS can be used as a tool for estimating Qpeak .