Because of increasing demanding for development of direct ecological landfill monitoring methods, there is a requirement for the condition of landfills and their influence on the environment to be characterized by the behavior of enzymes and bacteria mainly concerned with biochemical reaction in the landfills. This study was thus conducted to understand the fates of contaminants in association with groundwater quality parameters. For the study, groundwater was seasonally sampled from four closed unsanitary landfills in which microbial diversity was simultaneously obtained by 16S rDNA methods. Subsequently, a number of the specific genes of representative bacteria and encoding enzymes were quantified by real-time PCR. The relationship between water quality parameters and gene quantification were compared based on correlation factors. Correlation between DSR gene and BOD was greater than 0.8 while NSR gene and nitrate were related more than 0.9. For MTOT, it was at the highest related at 100% over BOD/COD and Dde genes were correlated over 0.8. In addition, anaerobic genes and DO were also related more than 0.8, showing anaerobic reactions generally dependent upon DO. As demonstrated in the study, molecular biological investigation and water quality parameters are highly co-linked, so that quantitative real-time PCR could be cooperatively used for assessing landfill stabilization in association with the conventional monitoring parameters.