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A Natural Ecological Wastewater Treatment System (NEWTS) is usually built on natural terrain with necessary topography modification to improve water flowing route and pattern, and then the topography modified NEWTS should also have a reasonable water storage volume and hydraulic retention time so as to achieve the anticipated water purification effect. In this study, the dynamic mesh technique based on the finite element method and element storativity coefficients was presented to develop a two-dimensional hydrodynamic and water quality model, which was used to optimize the design of NEWTS under the dynamic land-water boundary due to various water storage volume. The models were employed in the optimized design of NEWTS from a large abandoned coal mine, which purifies the polluted water flowing into a large water storage lake, as part of the East Route South-to-North Water Transfer Project in China. Specifically, the natural topography modification scheme was presented, and further, a reasonable water storage volume and hydraulic residence time was obtained, based on the reasonable estimation of roughness coefficient and pollutant removal rate of the NEWTS with phragmites communis.