"Waterproof" does not necessarily mean "works when submerged."
This paper seems to suggest that the JSN-SR04T will work when submerged.
Load up the NewPing library and the simple example sketch. Get the sensor working reliably in air first. Then find a body of water (such as a swimming pool or small boat harbor) that is approximately (30 to 40 cm x speed of sound in water / speed of sound in air) deep. Submerge the business end of the sensor a few cm deep and point the sensor at the bottom. If testing in a swimming pool, keep the sensor a meter or two away from the walls; if in a harbor, keep the sensor away from boats, piling, etc. Measure the depth with a tape measure, too (attach a weight to the tip of the tape if needed). Please report the measured depth and the sensor readings here.