Soil samples of both alluvial and acid sulfate saline were analyzed for their physico-chemical properties, microbial biomass and populations in the present study. Higher organic matter content with 1.88mg/mlwas noticed in saline (pokkali) than alluvial soil. The soil pH was slight variation from5.47 to 5.15. The contents of total nitrogen and sulfate are 0.09%and 0.0086%in alluvialwhere as 0.25%and 0.0072%in pokkali respectively. Themicrobial populations like heteotrophic, oligotrophic, aerobic and anerobic were enumerated on variousmedia. The alluvial soil had considerable population of aerobic heterotrophic bacteria and the diluted nutrient agar supported least number of the total aerobic heterotrophic bacteria whereas the soil extract agar had the highest populations. The population of diluted nutrient broth bacteria in alluvial soils was considerable whereas the population of nutrient broth bacteria in flooded alluvial soils was more than that of the DNB bacteria under aerobic conditions. On the contrarily, DNB were dominated under anaerobic conditions. In this study, flooded conditions are favorable for the build of oligotrophic bacteria especially those capable of growing under anaerobic conditions. The populations of anaerobic oligotrophic bacteria are also more than the population of aerobic oligotrophic bacteria. Hence the study explains the role of microorganism on the dynamic and mechanisms of nutrient mineralization and sustainability of this flooded agro ecosystems greater significance now the even before.