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Cigu wetland consists of industrial salt ponds and lagoon is situated at the coast in the southwestern of Taiwan which is demarcated as Coastal Nature Reserve. The salt ponds experienced declines in bird species diversity and population compared with those within the lagoon area due to the deeper water depths. Different kinds of measures to alter water depths of salt ponds by filling soil are proposed. The hydrodynamic simulations were conducted for studying the hydrodynamic response to proposed reconstruction alternatives. The potential waterbird abundance was then estimated for the alternative recommendation. The methodology proposed in this study can reduce the risk of unexpected results by implementing the reconstruction project directly.