The ball valve is supposed to be one-way...but it's not. It's supposed to close off when the diff cools and sucks in air suddenly, like a water crossing...but they get clogged, dirty, jammed, rusted, torn off, whatever, and then you get water in the diff.
If you think you're running water, pull the drain plug a little bit. If good oil seeps out, you're fine. If you're getting that thin gunky stuff, or straight water, flush it.
Also FYI if you did get a bunch of water in there, the best way to get everything out is free the rear axle (disco rear dshaft, pull ubolts is all you need to do), pull the fill plug and point the pinion up...do it after you've drained it normally, so you can clean any metal off the drain plug, then tilt it up and let it sit for a while.