Most electronics are unaffected by water when they are not energized. When an electronic device gets wet, it will usually be okay if you can cut power to it soon enough. This is not because the water will short it out like a hair drier in a bath tub. The voltages in typical devices like this are much too low for that. But rather because of the effects of water on ionized components.
I would recommend carefully taking the controller apart. Disconnect the battery. Even when the controller is off, there is some standby power running through some circuits.
If the toilet water was dirty, you should really clean off every part that already got wet with it with mild soap and water. If it already got wet, getting wet again isn't going to hurt it any worse, and you don't want any.. umm... residues left on anything. Since that would be bad.
After that, I would lay out the parts with a fan blowing on them. Give it a lot of time to dry out completely including all the little crevaces. If you don't open the controller... it's largely sealed, so the moisture that's seeped inside may never fully get out, and it will stay a humid environment inside.
The buttons and analog sticks and such will likely need to be cleaned just for mechanical reasons. I'm not sure if there are any light oils that Sony might be using that could have been washed away by the water. You might need to reoil them in spots using very light silicone. It may be that the whole assembly is normally dry with no lubricants at all. Certainly, you need to make sure that none of those surfaces are sticky, anyway.
Hope that helps.
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