Although various approaches have been proposed for the ecological restoration of water bodies such as rivers, lakes, marshes, and estuaries, it is essential to consider the connections among these water bodies in a watershed and explore sustainable management from a systems perspective. Watershed ecology treats a watershed, which is a natural hydrological unit, as a system, and explores the interactions that occur among social activities, economic activities, and natural eco-hydrological processes. This issue introduces new progress in watershed ecology and offers tools for managers to assess the effects of environmental changes on ecosystem health and to create strategies for ecological restoration from a systems perspective.