Water being drawn into the engine can cause serious damage but it is normally instant, it sounds like there is water sat in the manifold, but the fact it runs at all means there is probably no physical engine damage, if the water is pooled in the intake manifold or intake pipes there is a risk of it suddenly being drawn in and causing serious damage. All air intake pipework needs to be removed and checked and either remove and dry the intake manifold or use an endoscope camera to take a look inside to check.
whilst i was driving home the engine kept cutting out. when i took the air filter out it was wet. the engine runs but it will suddenly loose power then go back to normal. does this make your answer any different. i only drove through a shallow ford. the water was barely up to the wheel rims.
i was driving without the air filter (i know it is not ideal) when it kept loosing power.