As increasing attention is paid to surface water protection, there has been demand for improvements of domestic wastewater treatment plant (WWTP) effluent. This has led to the application of many different advanced treatment processes (ATPs). In this study, the treatability of trace organic pollutants in secondary effluent (SE) and associated biotoxicity reduction by four types of ATPs, including coagulation, granular activated carbon (GAC) adsorption, ultraviolet (UV) photolysis and photocatalysis, and ozonation, were investigated at the bench-scale. The ATPs showed different removal capacity for the 48 chemicals, which were classified into seven categories. EDCs, herbicides, bactericides and pharmaceuticals were readily degraded, and insecticides, flame retardants, and UV filters were relatively resistant to removal. During these processes, the efficiency of the ATPs in reducing four biological effects were investigated. Of the four biological effects, the estrogenic activity from SE was not detected using the yeast estrogen screen. In contrast with genotoxicity and photosynthesis inhibition, bacterial cytotoxicity posed by SE was the most difficult biological effect to reduce with these ATPs. GAC adsorption and ozonation were the most robust treatment processes for reducing the three detected biotoxicities. UV photolysis and photocatalysis showed comparable efficiencies for the reduction of genotoxicity and photosynthesis inhibition. However, coagulation only performed well in genotoxicity reduction. The effect-based trigger values for the four bioassays, that were derived from the existing environmental quality standards and from HC5 (hazardous concentration for 5% of aquatic organisms), were all used to select and optimize these ATPs for ecological safety. Conducting ATPs in more appropriate ways could eliminate the negative effects of WWTP effluent on receiving water bodies.