FREEWAT is a free and open source QGIS-integrated platform, developed to simulate several hydrological processes by combining the capabilities of GIS for geo-processing and post-processing tools with several codes of the well-known USGS MODFLOW ‘family’. FREEWAT platform was applied for the groundwater flow simulation of a coastal aquifer system, located in northern Greece. The simulation was conducted using the MODFLOW_2005 code, the Observation Analysis Tool (a FREEWAT module facilitating the integration of time series observations into modeling), while the UCODE_2014 code was used as the main module for the sensitivity analysis and parameter estimation. The statistics used include composite scaled sensitivities, parameter correlation coefficients, and leverage. The simulation of the investigated aquifer system was found to be satisfactory, indicating that the simulated level values were slightly greater than the observed values after the optimization.