In recent years, many projects have been carried out to enhance the durability of concrete structure from the influence of cracks. Generally, managing cracks should be a rather preventative method for sustainable development. Based on that, Bacillus subtilis natto - a local bacterium in Japan was found to have the ability to form CaCO3, which can be used as healing materials for cracks in the concrete structure. The bacterial biomineralization immobilized in lightweight aggregate was studied to improve the compressive strength by healing the cracks and densifying the structure. Moreover, as an essential parameter for durability enhancement, the water permeability of self-healing concrete through a water-flow system was carried out. Experimental results on the behavior of the materials indicate that Bacillus subtilis natto could lead the compressive strength to 40 % higher than the controls. Promising result in preventing the water through the cracks confirmed the self-healing effect with more potential in larger-scale.