In case of water retaining structures healing should occur under active flow conditions, with various water pressures and speeds of leakage. The present study was undertaken in order to evaluate the effect on crack repair of mortar by bacteria-based healing under active water flow. The mortar with the bacteria-based lactate-derived healing agent (HA) was added by 2% of cement mass. The results of the crack healing effect which was evaluated based on water permeability test were compared with normal mortar. The permeability test was carried out with various heights of water head. Disks with above 0.5mm crack in the middle was used as specimens. Consequently, the water flow rate increased as the water head became large, however it started to decrease as time goes by. It is probable that cracks will be repaired by bacteria-based healing under active water flow because the water tightness of with HA mortar reached 99%. On the other hand the tightness of normal mortar did not reach more than 97%. It was observed that the crack surface was healed by some material. from microscopic observation. The results of this study shows that the HA can be applied to crack repair system under active water flow.