Key hydrological factors such as water level, flow velocity, and discharge play a crucial role in regulating river and lake ecosystems. Based on extensive domestic and international research, and combining typical case studies, this paper systematically investigates the impacts of water level, flow velocity, flow rate, and hydrological connectivity on water environment and aquatic organisms. The regulation effects of these hydrological factors on ecological environment are analyzed. Water level influences the decomposition and transformation of pollutants in water and sediments, as well as the photosynthetic capacity of aquatic plants, by altering light intensity, redox conditions at the sediment-water interface, and the area of biological habitats. Changes in flow velocity and flow rate affect the suitability of biological habitats by modifying material transport capacity, sediment status, and the growth and reproductive needs of aquatic organisms, exhibiting significant threshold effects. Hydrological connectivity reflects the synergistic interactions and dynamic processes between hydrological elements, influencing the distribution of aquatic vegetation and the migratory and reproductive behaviors of fish. Finally, the paper introduces new technologies and methods used in related research and summarizes the current trends and developments in this field.