Numerical modeling systems are very important tools to study tidal inlets. In order to test its capability and accuracy of solving multi-inlet system problems, this study selected two widely used numerical modeling systems: Coastal Modeling System (CMS) and Delft3D Modeling Package. The hydrodynamics modules of the two modeling systems were tested at John's Pass and Blind Pass, Florida, a dual-inlets system, based on a similar modeling scheme. Detailed bathymetric surveys and hydraulic measurements were conducted to collect water depths, tide conditions, wave and current velocities as the input data as well as verification data for the models. A comparison study was conducted by comparing computed hydrodynamic results from both models with the extensive field measurement data. Results show that both of the modeling systems yield better prediction for water levels than for current velocity. Furthermore, under the similar modeling scheme, Delft3D was able to capture the measured tidal phase lag between the ocean boundary and the coastal inlet, therefore gave better water level prediction than the CMS model. However, the CMS yielded current velocities that are closer to the measured values than the DELFT3D model. CMS has a more user-friendly Graphic User's Interface (GUI) for input data preprocessing and plotting and visualization of output data. Delft3D has faster calculation speed.