The physicochemical factors and heavy metals in sediment before, during and after dredging of Niuqiaodi River in Wenzhou were investigated. The result showed that after the sediment dredging of Niuqiaodi River, the contents of TP, TOC and heavy metal in sediment were firstly decreased and then increased. The heavy metal contents in sediment reached the lowest level in one to three months after dredging. The contents of the pollutants in the river were significantly reduced after sediment dredging, but the improvement of water quality and sediment only lasts three to nine months. The evaluation results of the geoaccumulation index (I_geo) and the potential ecological risk evaluation indicated the sediments of Niuqiaodi River were seriously polluted by heavy metals and the sediment dredging contributed to reduction of pollution levels of heavy metals in sediment.