The main goal of this study is to evaluate the short-term and long-term inhibitory effects of Cu (II) on Anammox process. To investigate the short-term inhibition level, four different concentrations (1, 2.5, 5 and 10 mg L⁻¹ as Cu²⁺) were tested in batch reactors. IC50 levels for short-term exposure deduced as 4.57mg L⁻¹ (R²: 0.97) from the modified non-competitive inhibition model. Lab-scale continuous flow up-flow fixed bed reactor with Kaldness biofilm carriers was operated 240 days with gradually increased Cu concentrations (from 0.2 to 8 mg L⁻¹). To identify the IC50 levels in case of prolonged exposure of Cu(II), experimental data were fitted with a modified non-competitive inhibition model, and calculated as 6.77 mg L⁻¹ (R²: 0.95). The results show that the IC50 level for copper in long-term exposure was higher than in short-term exposure and the possible reason for that is the self-adaptation of Anammox bacteria.