Ultrasonic sensor underwater calibration
If I understand your question correctly, your problem is probably that the working range of the AJ-SR04M sensor is 20cm - 500cm. 

The sensor uses the same transducer to create the sound pulse and to listen for the echo.  It needs time to switch from one mode to the other, which explains why your sensor can't measure distances of less than 20cm.



The speed-of-sound in water is about 5x the speed of sound in air.  More specifically, at 20 degrees Celsius the speed-of-sound in air is approximately 343 meters per second, while the speed-of-sound in water is approximately 1482 meters per second.

This will cause the sensor to 'under-report' the distance in water.  The minimum distance will also be approximately 5x the minimum distance in air.



As an aside, you will also need to make allowance for the differences in the characteristic impedance and absorption between sound and water.

It's worth reading the paper Underwater Sound by P. Vigoureux (Proceedings of the Royal Society of London. Series B, Biological Sciences, Vol. 152, No. 946) for a discussion of all the factors involved.