This paper focuses on a collection of methods that can be used to analyze the water-energy-food (WEF) nexus. We classify these methods as qualitative or quantitative for interdisciplinary and transdisciplinary research approaches. The methods for interdisciplinary research approaches can be used to unify a collection of related variables, visualize the research problem, evaluate the issue, and simulate the system of interest. Qualitative methods are generally used to describe the nexus in the region of interest, and include primary research methods such as Questionnaire Surveys, as well as secondary research methods such as Ontology Engineering and Integrated Maps. Quantitative methods for examining the nexus include Physical Models, Benefit-Cost Analysis (BCA), Integrated Indices, and Optimization Management Models. The authors discuss each of these methods in the following sections, along with accompanying case studies from research sites in Japan and the Philippines. Although the case studies are specific to two regions, these methods could be applicable to other areas, with appropriate calibration.

The objective of this study is to describe a target water–energy–food (WEF) nexus domain world including causal linkages and trade-off relationships between WEF resources and their stakeholders, and to develop a WEF nexus system map as an interdisciplinary tool used for understanding the subsequent complexity of WEF nexus systems. An ontology engineering method, which is a qualitative method, was applied for the replicability of the WEF nexus domain ontology and the map, because ontology engineering is a method of semantic web development for enhancing the compatibility of qualitative descriptions logically or objectively. The WEF nexus system map has three underlying concepts: (1) systems thinking, (2) holistic thinking, and (3) an integrated approach at an operational level, according to the hypothesis that the chains of changes in linkages between water, energy, and food resources holistically and systemically affect the WEF nexus system, including natural and social systems, both temporally and spatially. This study is significant because it allows us to (1) develop the WEF nexus domain ontology database, including defining the concepts and sub-concepts of trade-offs relating to WEF for the replicability of this study; (2) integrate the qualitative ontology method and quantitative network analysis method to identify key concepts serving as linkage hubs in the WEF nexus domain ontology; and (3) visualize human–nature interactions such as linkages between water, energy, and food resources and their stakeholders in social and natural systems. This paper also discusses future challenges in the application of the map for a science–policy–society interface.

The value of a good is contingent on an individual’s experience that reveals the nature of the good. This study investigates the effects of a water shortage due to the Great East Japan Earthquake and Tsunami Disaster in 2011 on the voluntary management of community wells in the water-rich town of Otsuchi, Japan. A questionnaire survey based on a choice experiment (CE) framework was conducted in 2015 in which a total of 127 residents participated. The responses were then analyzed using two types of logit models that consider preference heterogeneity across survey participants. The results revealed that the severity and duration of the water shortage had opposing effects on people’s attitudes toward the wells. More specifically, increasingly severe water shortages due to the unavailability of water rendered people less supportive of the wells, whereas water shortages of a longer duration caused by limited access to water resources made people more supportive.

Island ecotourism development seeks to balance environmental protection with socioeconomic growth, promoting sustainable practices that benefit both local ecosystems and communities, which is a priority in ecologically sensitive regions such as Amami-Oshima Island. This study identified key factors in ecotourism using an optimized Driver-Pressures-State-Impact-Response-Management (DPSIRM) framework and integrated a System Dynamics (SD) model to develop a simulation system for island ecotourism development. The model was used to analyze the dynamic changes in ecotourism under various scenarios between 2010 and 2035. The results indicated that the Coordinated Development Model, which simultaneously enhanced tourism benefits and conserved natural resources, was the optimal strategy for achieving a win-win outcome. In contrast, the Socioeconomically Driven and Ecological Protection models revealed limitations in resource allocation: the former prioritized transportation infrastructure, resulting in insufficient tourism service provision, while the latter strictly limited development, thereby suppressing tourism and economic activity. This research deepens our understanding of complex dynamics in island ecotourism and reveals the effect of certain management outcomes through scenario simulations, offering policymakers effective support for informed decision-making.