The loss of coastal wetlands in Hong Kong Mai Po Nature Reserve adversely affected wetland-depended species. To mitigate this impact, gei wai ponds were reconstructed according to a set of biodiversity management zones (BMZs). This study, based on Canonical Correspondence Analysis (CCA), investigated if waterbird distribution was related to BMZ characteristics. Based on habitat characteristics, ponds in the same BMZ generally clumped in the same quadrant or within a short distance on CCA scatter plots, indicating that a BMZ zone produced common habitat traits. Ponds in a close distance on the plot had similar bird abundance or community structure. Significant correlations were noted between the abundance of cormorants and tall tree, and between waders and bare ground areas within study ponds. This study indicated that the control of key habitat factors was important for the success of reconstruction of gei wais and management of waterbirds in Mai Po.