i did some more investigation... it turns out that it's the water texture/mesh sliding away. this leaves big rectangular gaps where there is no water, but you can still see the land below which (i guess) has a shader that turns blue under 0km.
there is no water, but you can splash in these gaps and it gets you a splashing animation, just like if there was water. the problem appears when you go above 100km, but if you go even higher, at some point the issue solves itself, and then you can reentry in the same area without seeing anything wrong.
the issue may be the same as this reported bug: https://bugs.kerbalspaceprogram.com/issues/23902, only in that case it's on Eve.