The natural environment plays an integral role in achieving the Sustainable Development Goals (SDGs). Currently, freshwater ecosystems are experiencing significant impacts caused by human activities, including pollution, over-consumption, watering, alteration and reduction of runoff. These pressures are exacerbated by climate change. The aim of this research is to analyze the structure, functions and values of freshwater ecosystems of the Republic of Kazakhstan as a basis for ensuring their sustainability. This research studies the structure, features, types and main functions of aquatic ecosystems of the Republic of Kazakhstan; analyzes the current state and factors of impact on freshwater ecosystems; classifies modern methods of economic assessment of freshwater ecosystem services; considers examples of ecosystem services assessments of freshwater ecosystems in the world at different scales, as well as examines the main types of freshwater ecosystem services on the example of the Ile River.