The Yangtze River, the third largest river in the world, has been polluted by various organic chemicals. In 2018, China decided to implement ecological restoration of the Yangtze River to protect the river. However, except for some conventional pollution indices such as COD (Chemical Oxygen Demand) and NH₄⁺-N, the overall levels and risks of a wide variety of organic micropollutants (OMPs) in the Yangtze Estuary is not clear. Herein, results from a wide-range screening on levels and risks of OMPs in the Yangtze Estuary water were reported. 36 water samples were collected at 9 sites in the Yangtze Estuary in 2012 and 2013. Approximately 1200 OMPs were screened. A total of 131 OMPs were detected with total concentrations ranging from 1.8×10³ to 9.7×10³ ng/L. A tiered strategy was proposed to simplify the assessment of multi-substance ecological risks. Results showed that risk quotient (RQ) for 77% of the OMPs was less than 0.1. For 20 OMPs with RQ ≥ 0.1, joint probabilistic risks were assessed by species sensitivity distribution models. The joint risks as expressed by multi-substance potentially affected fractions are > 5%, and are not insignificant. The results may serve as a benchmark for protecting biodiversity in the Yangtze Estuary, as China motivated to have a fundamental improvement on the environmental quality by 2035.