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The necessity of an effective risk management in urban coastal zone increases, while the climate change creates unpredictable natural hazards. It is therefore very important to develop and implement analytical tools able to assist decision-makers to reveal vulnerable areas and prioritize relevant mitigation and adaptation measures. This article focuses on the applicability of the Coastal City Flooding Vulnerability Index (CCFVI) in zones of coastal cities belonging to the same country and incorporating industrial activities. It targets at investigating the capacity of the CCFVI to adequately take account of the impact of the industrial characteristics that are developed in the study areas on their vulnerability to coastal flooding. The results reveal the reduced discriminative capacity of the "administrative and institutional" subsystem in a centrally planned governance model like the one followed in Greece. They furthermore indicate the need for adding a separate indicators' subsystem, which will be able to measure the special features of the case study. Specifically, the industrial activity in the urban domain could severely impact the vulnerability of the area and should therefore be considered in designing the risk management plans for these areas. Moreover, the importance of weighting the indicators used in the vulnerability index calculation is emphasized.