Tailwater replenishment of urban river can not only solve the pollution problem caused by waste water to a certain extent, but also alleviate the shortage of water and hydrodynamic power in cities, which has significantly social, ecological and economic effects. Since the outbreak of COVID-19, the dosage of chlorine-containing disinfectant in tailwater has increased significantly, and the excessively residual chlorine had a potential impact on aquatic organisms. Haizhu Wetland belongs to the urban lake and river wetland of the delta, which contains 40 rivers and is the largest and best-preserved wetland ecosystem in Guangzhou. In this study, we selected typical streams in the Haizhu wetland for a long period of tracking observation. The physical and chemical index, the number and density of fish and benthic animals in the streams were measured during three periods: the suspension of tailwater discharge period (5-10, Aug, 2021), one month (10-13, Sep, 2021), and three months (15-18, Nov, 2021) after the tailwater was discharged, respectively. The stream that was not directly connected with the tailwater was selected as the reference point. Index of biologic integrity, redundancy analysis and other methods were used to explore the impact of continuous discharge of high residual chlorine tailwater on aquatic animals, and to evaluate the water ecological health status. The results showed that: (1) after the discharge of tailwater, the residual chlorine, total nitrogen and salinity in the water near the discharge outlet increased significantly. (2) With the continuous discharge of tailwater, adaptable and pollution-tolerant fish became the dominant species, while the number of dominant pollution-tolerant species in benthic animals decreased, and their density decreased significantly, especially in the streams near the discharge outlet. (3) According to the fish biologic integrity index, the water environmental quality were mainly sub-healthy and general in health, and had no significant difference among the measured sites. While by the benthic biologic integrity index, the water environmental quality near the discharge outlet changed from sub-health before discharge to sub-health and general in health after continuous discharge. There was no significant difference at other sites before and after tailwater discharge, mainly for health. (4) With the continuous discharge of tailwater, the effect of residual chlorine on benthic animals was more and more significant, but the effect on fish did not change obviously. In general, the continuous discharge of tailwater with high residual chlorine significantly changed the water quality and affected the survival of aquatic animals. Further studies are needed to explore the impact of tailwater discharge on other aquatic organisms and the specific influencing mechanism. In this study, the characteristics of community structure and biological integrity of fish and benthic animals before and after discharge of tailwater were discussed in detail. The study provided the theoretical and data support for water environmental health assessment and rational utilization of tailwater.