If things work in stand alone levels, I don’t see why a persistent would mess with them.
You may be doing something completely wrong like adding the water body to the persistent or working from within the persistent.
Load up and work the individual levels (go to unlit mode to see since they don’t have light).
then instead of loading into the persistent, open the persistent and just click play.
If you don’t crash, see if the levels look as expected or not.