The European Parliament has recently passed the “Nature Recovery” law to restore degraded ecosystems and prevent natural disasters as part of its “Biodiversity Strategy 2030” and “Green Deal”. In this respect, wetlands can provide a wide range of ecosystem services such as biodiversity conservation, hydrological land protection, provision of products, cultural and recreational benefits, and many others. However, they are still threatened by the expansion of agricultural land, overexploitation of water resources, water pollution, climate change, etc. Wetland conservation, however, is essential and requires coordinated action by managers, policymakers, stakeholders, and scientists. A systemic planning and design process is required to address these complex challenges. This research aims to outline an integrated, comprehensive, and well-structured planning framework for wetland systems that can be applied to different wetland types, in line with institutional wetland policy, governance, and management. The methodological approach developed in this study aims to integrate a longer-term strategy plan with a shorter-term action plan by combining the Yeomans scale of permanence and the Driver–Pressure–State–Impact–Response model. This innovative approach was applied to a specific case study and may guide further wetland planning in the future. The Nominal Group Technique was used, a consensus method aimed at achieving a general agreement and convergence of opinion. An expert group of seven members with different technical backgrounds was engaged and expert consultation was found to be a simple and rapid technique for carrying out wetland planning. The expert judgements were sound, consistent, and did not overlap (i.e., were not redundant). “Pressures” and “Impacts” were identified by the experts and clustered according to corresponding “States” and “Drivers”. Expert scoring allowed the resulting “Responses” to be ranked in terms of their relevance and influence on the development of the wetland strategy and action plan, while a priority order for their implementation was assessed according to the Yeomans scale of permanence. Agriculture was the highest rated ‘Driver’; similarly, Biodiversity (habitats and species) was the ‘State’ with the highest score. Therefore, their combination (agriculture and biodiversity) should be considered as the strategic cornerstone of the whole planning framework. This means designing and implementing a system in which agriculture and nature (in our case a wetland) are allied ecological systems in mutual compensation, according to the way natural elements are embedded in the agricultural system. A collection of factsheets containing the full list of responses considered in the Wetlands Action Plan, with detailed operational actions, is provided in the Appendixes.