In recent decades, human activities resulted in heavy metals accumulation in soil which is a threat to organisms' health. Nitrification process is one of the important biological indices to assess soil quality. This study investigates the nitrification process with complete randomized design in two calcareous and non-calcareous soils. Different treatments of nitrogen (0 and 100 mg/g), cadmium (0, 10 and 100 mg/g) and zinc (0, 100 and 500 mg/g) with 3 replicates were applied in the laboratory conditions. The results showed that increasing heavy metals concentration, nitrification rate decreased. Inhibition effect of Cd was more than the Zn. In the presence of ammonium at the highest cadmium concentration (100 mg/g) in the calcareous and non-calcareous soils, nitrification rate decreased 78% and 92% respectively. These values in the absence of ammonium were 75% and 90% respectively. Inhibition effect of the heavy metals on nitrification in the calcareous soil was more than the non-calcareous soil. Addition of ammonium to the Cd and Zn treatments led to three fold increase in nitrification rate. However, difference between nitrate values in the two soils, in the presence of ammonium was less than that of its absence. The most decrease in pH was observed in the 100mg Cd/g soil treatment with 1.3 unit. The findings of this research reveal that in the arid and semiarid soils, the CaCO3 can diminish the toxic effects of heavy metals on biological activities.