An experimental model was made on the improvement of sources water quality in the Huangpu River through the construction of a special aquatic ecosystem using ecological embankments. A 6 d retention time (RT) gave the highest removal rate capacity and benefit of micro-organic pollutants. Under these conditions, the removal rates were 70.5% atrazine, 57.7% dimethyl phthalate, 72.4% phthalic acid bis (2-ethylhexyl) ester, 62.4% diethyl phthalate, and 45.1% dibutyl phthalate. The varieties of micro-organic pollutants reduced from 51 to 28. In contrast, in the control pool with hard embankment, the removal rates only reached 40.2% atrazine, 42.9% dimethyl phthalate, 54.8% phthalic acid bis (2-ethylhexyl) ester, 52.0% diethyl phthalate, and 16.2% dibutyl phthalate. Through coordination of all constituent elements of special aquatic ecosystem, significant amounts of micro-organic pollutants were removed.