This study tested municipal sewage effluents generated at the pilot scale using conventional activated sludge (CAS), nitrifying activated sludge (CAS-N) and biological nutrient removal (BNR) in terms of the removal of trace organic compounds (TrOCs) and final effluent quality as indicated by yeast estrogenicity screening (YES), short term zebrafish reproduction and fathead minnow life-cycle tests. Under cold weather conditions (extended SRTs), the BNR configuration reduced the concentrations of the largest number of TrOCs while under warm weather conditions (reduced SRTs) the CAS-N was most effective. By comparison, YES test results indicated statistically lower responses in the BNR effluent in the warm weather tests and no difference between the effluents of CAS-N and BNR in the cold weather tests. Short term tests with adult zebrafish revealed no impact of the BNR and CAS-N effluents on egg production. By contrast egg production and gene expression in the CAS-exposed zebrafish were substantially less than that of control exposures and were similar to that of exposures to ammonia at similar concentrations as the CAS exposures. In fathead minnow life-cycle tests, exposures to CAS effluent (70-50% v/v) resulted in considerable mortality, reduced growth and reduced egg production that was likely due to the elevated ammonia concentrations. The CAS-N effluent (100% v/v) also resulted in some mortality and reduced growth and egg production in the fathead minnows. By contrast, the BNR effluent (100% v/v) had no effect on mortality, growth or egg production. The results suggest that enhancements to wastewater treatment plants that are associated with improved nitrogen removal can result in enhanced removal of TrOCs and can reduce the harmful effects of the effluents on aquatic biota.