||Governance of natural Common-Pool Resources (CPRs) is a central area of sustainability theory and practice. This arena generally lies at the interface between policy and science. Nevertheless, the conflict nature of CPR governance is often not systematically acknowledged in analytical approaches developed for the study of Social-Ecological Systems (SES) and specifically common-pool resources. This dissertation integrates three different bodies of scholarship—Institutional Analysis/Commons Theory, Political Ecology, and Societal Metabolism—and discusses the complementarities and potentials for bringing them together. Moreover, based on this theoretical discussion, it proposes an integrated and modified version of Elinor Ostrom's Institutional Analysis and Development (IAD) Framework. The dissertation illustrates the integration of the proposed modified version of the IAD Framework and its application to two case studies, both related to the governance of CPRs in conflict situations but significantly different in terms of geographical and political-economic contexts, institutional arrangements, and kinds of actors involved. Both cases are related to the ecological condition of critically important watersheds, and in both cases government plays a central role; however, the types of conflict and controversy show distinct characteristics. The two cases are not addressed in a comparative way but the take part in the same iterative theoretical/methodological/empirical process. In the first case, the resettlement programs in the Sanjiangyuan area (literally, three river heads) in Qinghai, People's Republic of China, are investigated. In order to preserve the Sanjiangyuan area, which contains the watersheds of the Yellow, Yangtze, and Mekong rivers, the Chinese central government has implemented since the year 2000 a program with the aim of resettling the total nomadic population and move them from the grasslands to new, semi-urban conglomerates, transforming their system of production from a predominantly self-subsistence pastoral mobile system to a sedentary system and promoting their integration into the market economy. In the second case, the policy-science interplay behind the geothermal development plans on Mount Amiata in Tuscany Region, Italy, is investigated. Mount Amiata is one of the most important freshwater reserves of central Italy. It has an aquifer that serves over 700,000 people in southern Tuscany and northern Lazio. However, independent studies, local environmental groups, and citizens associations point out that the geothermal activity is depleting and contaminating the Mount Amiata watershed and increasing the rate of degenerative diseases, morbidity, and mortality in the geothermal areas. This dissertation is presented as a hybrid between a "book format" and "collection of essays format. " It is developed in three parts. In Part I, the methodological, meta-theoretical, and theoretical background are discussed. Part II contains five stand-alone essays that relate to the applications and elaboration of the proposed modified IAD approach. In Part III, a conclusive discussion is presented.