Aquatic ecosystems are one of the most threatened ecosystems in the world resulting in the decline of aquatic biodiversity. Monitoring and the assessment of aquatic ecosystems are necessary to protect and conserve these ecosystems as monitoring provides insights into the changes in the aquatic ecosystem over a long period of time and assessment indicates the status of these ecosystems. This paper presents an overview of different methods for the hydromorphological, physical-chemical and the biological monitoring and assessment of surface waters. Furthermore, recently developed monitoring and assessment methods are discussed to support sustainable water management and contribute to the implementation of the Sustainable Development Goals 6 (SDG6 related to clean water and sanitation) and 15 (SDG15 related to terrestrial and freshwater systems) of the United Nations. However, many other SDGs are dependent on freshwater, such as food (e.g., SDG2) and climate-related SDGs. We presented an innovative concept for integrated monitoring and assessment. The main new elements are the monitoring of all communities and the use of integrated socio-environmental models to link these communities to ecosystem interactions and functions as a basis for determining their relation to the SDGs. Models can also allow to determine the effects of changes in SDGs on the different elements of the concept, and serve in this manner as tools for the selection of an optimal balance between the SDGs in the context of sustainable development.