The raw pigment-contaminated influent showed acute toxicity. The final effluent through A/A/O process still showed acute toxicity to D. magna and D. rerio. A mass of N-containing toxicants were detected in the pigment-contaminated wastewater. Semi-quantitatively analysis of 9 specific toxicants was performed with GC-MS. N-containing refractory toxicants were identified as the major acute toxicity source.