Ecological monitoring and assessment is fundamental for effective management of ecosystems. As an introduction to this Special Issue, this editorial provides an overview of "Ecological Monitoring, Assessment, and Management in Freshwater Systems". This issue contains a review article on monitoring surface waters, and research papers on data management, biological assessment of aquatic ecosystems, water quality assessment, effects of land use on aquatic ecosystems, etc. The papers in this issue contribute to the existing scientific knowledge of freshwater ecology. They also contribute to the development of more reliable biological monitoring and assessment methods for sustainable freshwater ecosystems and ecologically acceptable decision-making policies, and establishment of practices for effective ecosystem management and conservation.