The foundations of the methodology, methods of integrated assessment of the state and emergent properties (productivity, sustainability, environmental well-being) of complex natural systems are considered. The aim of the research was to summarize the results of the development and testing of models classifications of an integral assessment of the state, sustainability of terrestrial landscapes, water bodies and river systems and then, at the next stage, an integral assessment of their systemic well-being. Terrestrial landscapes, marine and lake systems and water catchment systems were selected as the objects of the study. The subjects of research were theoretical and methodological aspects and methods for constructing integral indicators of the state (integral indicator of productivity, integral indicator of environmental quality, etc.), integral indicators of sustainability, integral indicators of well-being (health) of land, lake and river systems. The basics of the methodology for assessing the state, stability and wellbeing of terrestrial and aquatic geosystems are considered, as well as the integral estimation algorithms; the results of assessment studies: an integrated assessment of the trophic status of water bodies; integral assessment of the resistance of water bodies to changes in the parameters of the natural and anthropogenic regimes; paleoreconstruction of hydroecological conditions on the Laptev Sea shelf based on integral indices; integral assessment of the ecological status and ecological well-being of reservoirs, watercourses, water catchment systems; integral assessment of the sustainability of terrestrial landscapes; integral assessment of the stability of a sociological system with a hypothetical change in the quality of the environment on the example of northern regions of Russia. Research was focused on the development of multi-criteria and multilevel classifications for the study of the emergent properties of complex systems in nature and society and the construction of integral indicators based on Analysis and Synthesis of Indicators for Information Deficiency (ASIID) and Aggregated Preference Indices System (APIS) methods and models.