I have this cool idea on using the HC-SR04 Ultrasonic Sensor to measure the depth of water would that work?
By depth, do you mean the surface level relative to the sensor, or the distance between the surface and the bottom (as in a sounder or fish finder)?
Measuring from the surface level to the bottom.
I don't think those sensors will work well underwater. If at all.
Any other suggestions though?
Google for ultrasonic transducers.
Why don't you take one for the team and try it?
Cover the nozzle with cling film and stick it just under the surface, adjust the code for speed of sound about 1500m/s, see what happens......
If you're going to do that, at least submerse the transducers. The coupling from air to water is going to be terrible otherwise. Another thing... Some of those cheap flat piezo transducers might reach the necessary frequencies. A long time ago I read an article about using those for water immersion. You should silicone around the edges and waterproof the surface with some kind of spray on lacquer, or maybe wax? Those were for underwater sound recording.