This study deals with the information gap on desertification risk for wetland habitat types in Natura 2000 network sites of Greece. Using the Environmentally Sensitive Areas (ESA) index as a proxy, all Natura 2000 wetland habitat types have been assessed and assigned to desertification risk categories. The assessment was conducted at the national, regional, and local scales in order to provide different outcomes for targeted support on decision and policy making regarding restoration and conservation measures. The main results document that circa 20% of wetland habitat types area are considered under desertification risk, while circa 10% are considered as potentially affected by desertification. It was also shown that there should be prioritization of the habitat types that need attention due to their inclusion in the different desertification risk categories. The study also highlights the administrative regions (NUTS2) and Natura 2000 sites and the need to structure, draft, and implement conservation projects to mitigate wetlands’ risk as well as the use of wetlands as primary nature-based solutions (NbS) in the battle with desertification and climate change. Management implications are also provided from the perspective of habitat restoration as well as for their exploitation as valuable NbS for biodiversity conservation and ecosystem services maintenance.