How to make macro photography when the subject is placed in shallow water?

A polarizing filter is a must. At the right angle, 100% of the light reflected by the water is polarized in one direction. You can null this out by rotating the filter appropriately.

Proper lighting minimizes reflections off the water surface in the first place.

Another thing to consider is color balance. Put a known white object in the water next to your subject, and photograph that with the same lighting and setup you will make the real photographs of the subject with. Then correct for that to be white in post-processing.

You can use camera caser for your camera and lens like this or u can use the polarize filter. The case is like this: