Sulfate-reducing passive bioreactors treat acid mine drainage (AMD) by increasing its pH and alkalinity and by removing metals as metal sulfide precipitates. In addition to discharge limits based on physicochemical parameters, however, treated effluent is required to be nontoxic. Acute and sublethal toxicity was assessed for effluent from 3.5-L column bioreactors filled with mixtures of natural organic carbon sources and operated at different hydraulic retention times (HRTs) for the treatment of a highly contaminated AMD. Effluent was first tested for acute (Daphnia magna and Oncorhynchus mykiss) and sublethal (Pseudokirchneriella subcapitata, Ceriodaphnia dubia, and Lemna minor) toxicity. Acute toxicity was observed for D. magna, and a toxicity identification evaluation (TIE) procedure was then performed to identify potential toxicants. Finally, metal speciation in the effluent was determined using ultrafiltration and geochemical modeling for the interpretation of the toxicity results. The 10-d HRT effluent was nonacutely lethal for O. mykiss but acutely lethal for D. magna. The toxicity to D. magna, however, was removed by 2 h of aeration, and the TIE procedure suggested iron as a cause of toxicity. Sublethal toxicity of the 10-d HRT effluent was observed for all test species, but it was reduced compared to the raw AMD and to a 7.3-d HRT effluent. Data regarding metal speciation indicated instability of both effluents during aeration and were consistent with the toxicity being caused by iron. Column bioreactors in operation for more than nine months efficiently improved the physicochemical quality of highly contaminated AMD at different HRTs. The present study, however, indicated that design of passive treatment should include sufficient HRT and posttreatment aeration to meet acute toxicity requirements.