Shooting insects in shallow ponds

A place to start is with a polarizing filter to allow removal of reflections off the surface of the water. It’s probably simplest if this is hand held between the phone and the water. The user can rotate the filter as required to remove glare. Polarizing filters are commodity items, so costs can be low.

Due to the small size of phone camera sensors, depth of field is less likely to be a problem than with a DSLR.

If depth of field is a problem, a point and shoot camera with a zoom lens might be worth considering...small sensors will provide greater depth of field than larger. And a hand held polarizing filter can be held in front of the lens at least as easily.

The issue is how to sustain a deep DOF so that the body of water from surface to the bottom is all in focus. The AF tends to focus on the surface with the bottom out of focus, or vice versa.

Very few cell phones have the ability to actually change the aperture of the lens; so your ability to set/control the DoF will be limited. However, the very small sensor size combined with short focal lengths makes that less problematic.

What is more the problem is the placement of the DoF, as you noted. To overcome that issue you will need to use manual focus and focus halfway below the surface. Luckily, most android phones offer manual focus. If the default app doesn't have the function many third party apps do, and there is an app to check if your phone is capable as well. https://geekydevs.com/

But you might be better off choosing a small sensor "tough" type of camera (Ricoh WG-70, Olympus TG-6, etc) that offers more than just manual focus (macro/micro modes, aperture control, etc) and is waterproof as well. Obviously, the more options you want the more it's going to cost; but still relatively cheaper than a cell phone, which may well need replaced should it go for a swim.

IMO, you will be better off blocking unwanted reflections from the surface as opposed to using a polarizing filter. With these sensors/situations the loss of light a polarizer causes can be quite problematic.