Redox-mediators such as syringaldehyde (SA) can improve laccase-catalyzed degradation of trace organic contaminants (TrOCs) but may increase effluent toxicity. The degradation performance of 14 phenolic and 17 non-phenolic TrOCs by a continuous flow enzymatic membrane reactor (EMR) at different TrOC and SA loadings was assessed. A specific emphasis was placed on the investigation of the toxicity of the enzyme (laccase), SA, TrOCs and the treated effluent. Batch tests demonstrated significant individual and interactive toxicity of the laccase and SA preparations. Reduced removal of resistant TrOCs by the EMR was observed for dosages over 50 μg/L. SA addition at a concentration of 10 μM significantly improved TrOC removal, but no removal improvement was observed at the elevated SA concentrations of 50 and 100 μM. The treated effluent showed significant toxicity at SA concentrations beyond 10 μM, providing further evidence that higher dosage of SA must be avoided.