In order to monitor changes in the concentrations of metals in the soil, different microbial indices such as BIOLOG, microbial carbon (C(mic)), basal respiration, and culturable microbe's most probable number were used. We compared these methods and wanted to discover which method was the best at measuring slight changes in the amounts of heavy metals. Factor analyses were applied to the BIOLOG data and metal concentrations so the combined effects of heavy metals on microbes could be analyzed via statistical data reduction and the distribution patterns of metal concentration could also be revealed. The results showed that the BIOLOG method could barely detect subtle characteristic changes in the soil samples, while the C(mic) method was more sensitive. Furthermore, different heavy metals did not have the same origin/source, and their effects on microbial indices should be analyzed separately. Significant positive correlations between C(mic) and metals were observed and suggested the limitation of using traditional microbial parameters as metal pollution indicators. Among all the soil characteristics in our study, pH seemed to be the most active abiotic factor that affected microorganisms.