Coastal flooding events pose a critical risk in delta areas, since they are characterized by population growth and urban expansion. A better understanding of Extreme Water Levels (EWLs), the mechanisms generating them, and their components, i.e., astronomical tide and storm surge is of great importance as they drive the maintenance and design of flood protection systems. Therefore, a statistical investigation of them can provide new insights for more reliable flood risk mitigation infrastructures. In this study, we analyse these components and compare different probabilistic methods i.e., univariate extreme value analysis, copula functions, and Joint Probability Method (JPM) for the better estimation of EWLs. We use Hoek van Holland (NL) as a representative case study, since the dynamic conditions of this deltaic environment with man-made infrastructures render the area of strategic importance. The results indicate that a more accurate estimate of the declustering time between extreme events can be achieved using correlation of high surges and high wind speeds, taking into consideration also the wind direction. In the Southwest Delta this time estimated to be around 4 days. Furthermore, the EWLs components, i.e., surge and astronomical tide, show negative dependence. From the comparison between statistical approaches to model EWLs, results show that EWLs estimated via EVA and JPM do not vary significantly, while copulas’ seems to outperform the other methods. However, the selection of the proper copula to show the dependence is critical. As a conclusion, the analysis of the dependence between tides and storm surges can lead to more robust inferences of EWLs.