Laboratory evaluations were conducted to study the toxic responses of heavy metals such as copper and nickel of an autotrophic culture of strict nitrifiers (Nitrosomonas sp. and Nitrobacter sp.) in continuous flow stirred tank reactors (CSTR). One of the CSTRs was operated as a suspended growth (SG) system while the other was operated as an attached & suspended growth (A&SG) system. Nitrification inhibition in a SG and A&SG systems was investigated with the emphasis on the effect of shock loading of copper and nickel. As a result of the copper and nickel test, Nitrosomonas sp. was found to be equally or more sensitive than Nitrobacter sp. However, a higher influent nickel concentration of 50 mg/L was needed to cause a similar percent inhibition of ammonium oxidation than the copper concentration of 5 mg/L. A geochemical equilibrium speciation model, MINTEQA2/PRODEFA2, was used to compute the concentrations of various chemical species present in the wastewater for both systems. The high correlations of Cu(NH3)4+2 and Ni(NH3)4+2 with percent inhibition were found and it was thought that they were probably the species responsible for the inhibition of ammonia oxidation.