In recent years, water pollution accidents resulting in acute aquatic ecological risk and security issues become a research focus. However, in our country, the surface water quality standards and drinking water health standards were used to determine the safety of waters or not in pollution incidents due to lacking safety effect threshold or risk value for protection of aquatic life. In foreign countries, although predicted no effect concentration (PNEC) or risk value (R) of pollutants were provided for protection of aquatic organisms, the PNECs or risk values were derived based on long-term exposure toxicity data NOECs (no observed effect concentrations) and lack of short-term exposure risk or threshold values. For the short-term and high dose exposure in pollution incident, ecological risk assessment methods were discussed according to the procedures of the conventional ecological risk assessment and the water quality criteria establishment of the U.S. EPA for the protection of aquatic organisms in short-term exposure, and had a case study. At the same time, we provide some suggestions for the establishment of ecological risk assessment system in water pollution incidents.