In view of the severe problems of serious pollution of urban river waters and intensified damage of water ecosystems, the Niushoushan River in Jiangning District of Nanjing City was taken as an example, 11 water ecological evaluating indicators were selected by monitoring the changes of water quality, phytoplankton, benthic animals and heavy metals. In order to reduce the influence of subjective factors on the determination of index weights, the entropy method-material element extension evaluation model was used to evaluate the water ecological security status of the Niushoushan River. The results showed that the water quality of Niushoushan River is moderate, the algae density far exceeds the standard limit, and the biodiversity is poor. The comprehensive assessment level of water ecological security status is between IV and V, which is consistent with the actual situation. This study helps guiding the water ecological restoration and protection in Jiangning District.