In this study, we have investigated the antimicrobial effects of bacterial strains isolated and characterized from cooling water towers and biofilms niches of green biocide obtained from the plant Boerhaavia diffusa plant extract. Initially we have enumerated the viable bacterial cells from cooling water and biofilms of mild steel (MS1010). Various strains of heterotrophic bacteria that are isolated from viable bacterial colonies include iron oxidizing bacteria (IOB), Manganese oxidizing bacteria (MnOB), acid producing Bacteria (APB). Morphology of the isolated bacterial cells showed circular cells, slight yellow and gram positive rod cells. Specifically we have identified the selective bacterial cells as SKR-4 and SKR-7. Furthermore we have confirmed that the isolated strains SKR-4 and SKR-7 were capable of inducing corrosion of mild steel (MS1010), and it was confirmed using FITR and electrochemical studies like weight loss, polarization studies. Later we have tested the antibacterial effect of green biocide obtained from Boerhaavia diffusa and it was observed that 50 PPM green biocide was optimum for antibacterial effect of Boerhaavia diffusa. Also the same dose 50PPm was capable of inhibiting the formation of biofilm and extracellular polymeric substances (EPS). Taken together, our results showed that Boerhaavia diffusa plant leaf extract has the ability to inhibit the corrosion of mild steel (MS1010) and it is due to its antimicrobial efficacy and ability to inhibit the formation of EPS. However, our results are preliminary and further studies may be required to understand its mechanism of antibacterial action and to improve its efficacy on large scale levels.