Water in the transmission...

Depends on how long the water sat in there. If only a week or so you should be fine. However, might take a couple fluid changes to get it all flushed out. Drain your converter too, that will help speed up the process.
I had a friend give me a couple 727's that sat outside for years full of water. I was really surprised at how many parts were salvagable in them. Valve bodys were trash and so were the pans, everything up higher survived ok.