But it's fine from outside the water? If it's custom water (doesn't ship with stock TF2) it's probably missing its bottom material. If it's a stock material more than likely some files became corrupt. Validate the TF2 files via Steam with all TF2 related stuff closed, then try again.
If the water is invisible in its entirety either VVIS was deliberately not run (water needs VVIS to work) or you have a leak.