The geological conditions of the contaminated sites will affect the migration of microorganisms in the underground environment. In order to study the effect of low-permeability lens on bacterial transport, green fluorescent protein labeling combined with light transmission method was used to reveal the bacterial transport in the heterogeneous aquifer. The experiment has the advantages of real-time monitoring and no disturbance. The results showed that the bacteria gave priority to bypass the lens to flow away. The lens had a significant effect on hindering the bacterial transport due to adsorption and straining. The larger permeability coefficient ratio between the bulk media and the low-permeability lens was, the more obvious the obstruction was. AN-1 cannot enter the lens until the ratio decreased to the order of 102. With the increase of the flow velocity, the bacterial plume changed a lot. The higher flow velocity reduced the adsorption and retention of AN-1 to the media, resulting in some microorganisms remaining in the pores washed down. When the flow came to 2.0 m·d-1, AN-1 cannot adhere to the media due to the excessive fluid shear stress.