Disclosed are an apparatus for sampling water in a borehole and a method thereof. The apparatus includes a water sampling cylinder to sample the water in the borehole; a first camera to monitor the water sampling cylinder and a sample discharging part provided in the borehole; a first motor to insert the water sampling cylinder into the sample discharging part; a vacuum vessel to receive a sample input from the water sampling cylinder; a waterproof member having a hole serving as a passage through which the water sampling cylinder moves back and forth; and a supporting member that urges the waterproof member closely to the sample discharging part to prevent foreign substances from being introduced into the borehole. The first motor includes a plurality of protrusions meshed with a plurality of grooves provided in the water sampling cylinder.