Would wading knee-deep in water (in this case, in a shallow pool inside a cave complex where the floor beneath the pool is rock with bits of sand) cause a character to be flat-footed?
Just call it difficult terrain and be done with it. If the floor under the water was particularly slimy (but you've said it's rock and sand), declare that it is treated as a non-magical permanent "grease" effect in a particular area.