Abstract Optimum water depth is critical for wetland restoration as it directly influences the distribution, growth and adaptability of wetland vegetation, community structure, and water bird habitat selection. Reed marshes are the main habitats for water birds, especially for the endangered oriental stork Ciconia boyciana in the Yellow River Delta, China. In this study, we determined the optimum water depth threshold based on: (1) the ecological adaptability of the reed Phragimtes australis along the water gradient of the delta and (2) the preferences of C. boyciana for specific habitat characteristics in different seasons, from March to October 2009. The results showed that the optimum water depth thresholds in areas with shallow water and dry land are [0,5.7] cm and [-1.3, 0] cm in spring, [5,29.8] cm and [-3.7, 0] cm in summer, and [3.3, 27.5] cm and [-7.7, -3.1] cm in fall, respectively. Our data indicate that future studies should focus on optimum water level and water volume thresholds as practical measures for wetland restoration and protection.