All the regulations that define a maximum concentration of metals in the receiving soil are based on total soil metal concentration. However, the potential toxicity of a heavy metal in the soil depends on its speciation and availability. We studied the effects of heavy metal speciation and availability on soil microorganism activities along a Cu/Zn contamination gradient. Microbial biomass and enzyme activity of soil contaminated with both Cu and Zn were investigated. The results showed that microbial biomass was negatively affected by the elevated metal levels. The microbial biomass-C (Cmic)/organic C (Corg) ratio was closely correlated to heavy metal stress. There were negative correlations between soil microbial biomass, phosphatase activity and NH4NO3 extractable heavy metals. The soil microorganism activity could be predicted using empirical models with the availability of Cu and Zn. We observed that 72% of the variation in phosphatase activity could be explained by the NH4NO3-extractable and total heavy metal concentration. By considering different monitoring approaches and different viewpoints, this set of methods applied in this study seemed sensitive to site differences and contributed to a better understanding of the effects of heavy metals on the size and activity of microorganisms in soils. The data presented demonstrate the relationship between heavy metals availability and heavy metal toxicity to soil microorganism along a contamination gradient.