The increasing pressure on water resources in Europe’s broader area led member states to take measures and adopt a common legislative “umbrella” of directives to protect them. The aim of this research is to investigate practicing deficiencies, information lacks and distances from optimal status as set by the Water Framework Directive and supporting water uses. This contributes to the improvement of the efficiency and harmonization of all environmental goals especially when management of Protected Areas is addressed. Gap analysis, an approach that reveals the distance between current and desired level, was carried out, targeting five Mediterranean hydro-ecosystems, covering three major water policy pillars “Monitoring Practices”, “Management Practices” and “Water Quality and Pressures”. Data for such analyses was collected by literature research supported by a query matrix. The findings revealed a lack in compliance with the Water Framework Directive regarding the “Monitoring Practices” and several deficiencies in sites burdened by eutrophication and human pressures on “Water Quality and Pressures” field. As for “Management Practices”, extra effort should be applied in all hydro-ecosystems to reach the desirable state. We suggest that gap analysis, as a harmonization tool, can unify apparently different areas under the same goals to reveal the extra necessary “investment”.
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