The pothole is one of the special habitats in river ecosystems, which is simply structured, well-defined, food chain-short, and easily controlled, thus making it a model system in ecological, evolutionary and phenological studies. Here we first reviewed hydrological, chemical and physical characteristics of potholes, their biological community (biodiversity, environmental factors) as well as food chain (competition, predation and parasitism) in mountain rivers. The differences between pothole ecosystems and river ecosystems in hydrological characteristics, biological community and food-chain were analyzed. Hydrological, physical chemical, and ecological characteristics of potholes were largely unexplored in China. Finally, we suggested future directions and recommendations in pothole ecosystems.