The dispersion of nitrogenous compounds and heavy metals into the environment is frequent during mining activities. The effects of nickel (Ni) and cobalt (Co) on denitrification of simulated mine waters were investigated in batch bioassays and fluidized-bed reactors (FBRs). At pH 7, batch tests revealed that Co did not exhibit inhibition on denitrification even at 86.6 mg/L. Ni showed to be inhibitory at 50 and 100 mg/L by decreasing nitrate removal efficiencies of 18 and 65 %, respectively. In two FBRs, operated at 7–8 and 22 °C, 5.5 mg/L Ni did not affect nitrate and nitrite removals because of FBR potential of diluting soluble Ni feed concentration. On the contrary, the effluent pH clearly decreased in both FBR1 and FBR2 because of nickel sulfide precipitation and Ni inhibition of the last two steps of denitrification. When Ni injection was stopped, the process recovered more slowly at 22 than 7–8 °C. This is the first study reporting the effect of Ni on denitrification in biological FBRs.