Coastal ecosystems are among the most economically valuable and highly threatened on Earth; they provide valuable ecosystem services (ESs) but are severely exposed to climate changes and human pressure. Although the preservation of coastal ecosystems is of the utmost importance, it is often sub-optimally pursued by Governments and Societies because of the high costs involved. We consider salt-marsh ecosystems in the Venice Lagoon as an example of a threatened landscape, calling for innovative, integrated management strategies, and propose an application-driven methodological framework to support policymakers in the identification of cost-effective incentive policies to ecosystem preservation. By combining group decision-making and Value-Focused-Thinking approaches, we provide a multiple-criteria decision model, based on pairwise comparisons, to identify which ESs are top-priority policy targets according to a cost-effective perspective. We implemented an online Delphi survey process and interviewed a pool of experts who identified “recreation and tourism”, “coastal protection from flooding”, “carbon storage”, “biodiversity and landscape”, and “nursery habitats for fisheries” as the five most relevant ESs for the Venice Lagoon taking into consideration the Environmental, Economic, and Social perspectives. Our results suggest that the Environmental perspective is the most important criteria, whereas “biodiversity and landscape” is acknowledged as the most important ES.