The present paper describes a methodological framework that combines ecosystem services (flood protection, education, art/culture, recreation and tourism) with economic analysis for selection of multifunctional measures for flood resilience. The framework includes active stakeholder participation and it consists of the four main components: (1) identification and valuation of ecosystem services pertinent to the project site under various mitigation scenarios, including baseline (pre-mitigation conditions); (2) evaluation of most effective flood mitigation measures through hydrodynamic simulations, and evaluation of economic viability using cost-benefit analysis; (3) selection of measures through consideration of ecosystem services, and solicitation of stakeholders’ inputs; (4) development of the conceptual landscape design. Application of the framework was demonstrated in a case study of Ayutthaya Island, Thailand. Results of our research suggest that taking a holistic perspective of ecosystem services and economic assessments, marshalled through active stakeholder participation, has the potential to achieve more ecologically sustainable and socially acceptable solutions for flood protection in areas with cultural heritage. However, there is still a considerable challenge in taking this framework to a full-scale practical implementation, and this mainly relates to the selection of indicators that can enable proper application of ecosystem services.