Water is the substance that made life on Earth possible. It plays a key role in both the individual and population development of all species. Water is also a critical resource for humans as populations continue to grow and climate change affects global and local water cycles. Water is a factor limiting economic development in many regions of the world. Under these conditions, good water quality becomes an extremely important factor that determines its economic utility, including water supply, recreation, and agriculture. Proper water quality maintenance of freshwater ecosystems is also very important for preserving biodiversity. The quality of water depends on many factors, the most important of which are related to human impact on water ecosystems, especially the impact of various pollutants from municipal economy, industry and agriculture. Hydrotechnical changes, such as river damming, drainage processes and water transport between catchments also have a significant impact. Water quality is also dependent on the impact of natural conditions connected, e.g., with climate, catchment, water organisms and their interactions within the food-webs, etc. This Special Issue consists of fourteen original scientific papers concerning different problems associated with the water quality of freshwater ecosystems in a temperate climate. Most of the articles deal with the relations between water quality and the structure of ecosystem biocenoses. The conclusion of these articles confirms the fact that the deterioration of water quality has a direct impact on the quantitative and qualitative structure of biocenoses. This is accompanied by a decline in biodiversity and the disappearance of rare plant and animal species. They also draw attention to the particular importance of internal physical and chemical differentiation within the aquatic ecosystem, both in horizontal and vertical dimensions. The problem of ensuring proper ecological conditions and good quality of water in freshwater aquatic ecosystems is also raised, and methods for the restoration of water bodies are presented. The majority of the research presented in this Special Issue was carried out in Central Europe, and one of the papers concerns the area of West Africa—the edge of temperate climate zone.