Hey kevin, great to see a sketch.
1) I would ensure a standard measuring tape on the outside of the tube – make it easy for any site visits by anybody the waterdepth and time of measurement can be recorded and used to validate/calibrate that electronic measurements
2) I personally have no experience with the ultrasonic transducer method – so I would think you want to be pretty clear that it works, and also to define what accuracy of measurement you are looking for. A simple way is to make the equipment and then leave it with a known stable water column for a couple of weeks. Possibly even allow water to evaporate and verify the readings as the water drops.
3) Might be better to move the senors at the bottom into their own protective shielded pipe so that if they ever need maintenance you don’t risk moving the pipe with the water column in it.
4)I would think for your flood location, you want to be aware of the velocity of the water and whether or not the top of your standpipe needs tying into the bank. A visual examination of local conditions for a low velocity location is always best.
Here is a link with some pictures of people installing a pipe in tidal marsh area.
Usually with any electronic sensor the quality of the recordings – errors is the most challenging. Be great if you report on what you find if you do any managed “soak” testing.