Since my 997.1 was new, water was always getting to fan belts (two squeaky ones & one mass air sensor replaced). Dealer called it just a factory squeak to live with.
Surgeon says issue gone on 2008, so problem may have been corrected.
Putting a mat over engine while washing stopped nothing much which got me wondering.
Placed newspaper on engine during wash and found water is running in from bottom of rearglass....this drain water is flowing directly into the engine compartment at mutiple points.
Water floods in if engine lid open, but water is slowed down some, with lid closed so the metal to metal close-contact stops maybe 60-75% of the water flow noticed with engine lid open.
This has to be factory blemish that could be corrected if Surgeon right.
Will call Porsche on Monday to see their solution. Might be tough to replace rubber seal at bottom of the glassI guess when driving in the rain, water is pouring all over the engine but evaporates quickly with heat. Doesn't seem like a smart design.
However, maybe simpliest fix is to just fill entire 3 -ft opening with 1/2" weatherstripping if Porsche has no solution.
In theory, looks like water is allowed to exit at far ends of the glass bottom and run down to two drain funnels on left and right side of the car body that engine-lid shuts down on. This drain water then exits to pavement. However, with my turbo, water is escaping all along 3-foot span, that is, through the sides of the rubber seal and pouring directly into engine compartment.

 

I noticed that after the first few times i washed my car. The majority of the water comes in from where it runs off the rear glass and right into the engine, between where the rear deck lid meets the glass. The rest comes in through the fan. I asked my service advisor he said the engine is designed to get wet. I don't know how that could be ok for the car but I assumed the engineers at Porsche in their cold and wet weather testing would have noticed that. So anyway, I lay a towel down on my engine and close the lid every time I wash it. The belts still squeak a little after because you have to open the lid and remove the towel before you turn the engine on and water drips in, but is sure a hell of lot better than soaking the engine. I was actually very surprised that no one else besides me and you have complained about this on this forum. I guess few guys wash their own cars . Anyway, if you find out a solution, please let us know.

 

This water-engine issue has been discussed several times on 6speed and Rennlist, but no one mentioned the bottom-window seal except you this time. Now, I put a 1/2 piece of wheatherstrip on the bottom opening of glass and a mat on engine cover and no water ends up in engine compartment when washing the beast. Still bet there is an upgrade on that rear window seal if the 997.2 doesn't seem to have that problem (Surgeon comment) and will check with Porsche in morning. That dealer is a bit naive and lazy to say that engine is designed to get wet. Mine lost 2-drive belts and a mass air sensor because of water in engine compartment.

 

I know you can't do much about rain getting into the engine bay but why use a hose when you're washing when you know water will get in that way. I use the two bucket method with ONR and never have any issues with water in the engine. I never spray the back of the car.