Large volumes of contaminated water are produced via intentional and unintentional incidents, including terrorist attacks, natural disasters and accidental spills. Contaminated waters could contain harmful chemicals, which present management and disposal challenges. This study investigates three Advanced Oxidation Processes (AOPs) - UV/H2O2, O3/H2O2, and electrochemical oxidation using a boron-doped diamond (BDD) anode - to treat eleven contaminants including herbicides, pesticides, pharmaceuticals, and flame retardant compounds. To address treatment and toxicity concerns, this study focuses on the resulting microbial toxicity via Microtox® toxicity and Nitrification Inhibition tests. The results suggest four functional Microtox® toxicity categories upon AOP treatment, which are useful for streamlining AOP selection for specific applications. Except for one compound, the O3/H2O2 and UV/H2O2 AOPs achieved, within experimental error, 100% parent compound degradation during 2 h of treatment for all contaminants, as well as Microtox® toxicities that declined below 10% by the end of the treatment. In addition, anodic oxidation with a BDD electrode exhibited slower degradation and some increases in Microtox® toxicity. Only one compound exhibited above 50% Nitrification Inhibition, indicating the robustness of activated sludge to many contaminated and AOP-treated waters. These results indicate that AOP pre-treatment can be a viable strategy to facilitate drain disposal of contaminated waters, but that eco-toxicity may remain a concern.