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The bio-clogging using bacteria can be an eco-friendly and sustainable alternative to conventional grouting methods for seepage control. However, it remains unclear to date how the dilute concentration of bacterium and medium during field installation can affect the setting time of bacterium and its correlation with permeability reduction. In this study, the setting time of bacterium and its effectiveness in permeability reduction were addressed through experimental and theoretical investigations. A series of sand column was cultivated using different concentrations of Leuconostoc mesenteroides and culture medium. The distribution and composition of the bacterial product (i.e. dextran) were observed by refractometer, scanning electron microscope (SEM), and energy dispersive X-ray spectroscopy (EDS). Soil permeability was recorded using a constant head test. The results revealed that bacterium was effective to produce dextran at the setting time of about 5 d after installation. This dextran can reduce the permeability of bio-mediated soil by two orders of magnitude, even without culture medium supply. In general, the dextran production decreased proportionally with increase of bacterium and medium concentration. However, at 50% bacterium and medium concentration by weight, it still has a significant influence on permeability reduction with similar setting time, compared to 100% concentration.