Very common problem (especially if the car lives outside or is used in the rain, road debris gets washed down the drain holes and blocks them, then the next time it rains the drain holes overflow and water gets in the car).
997 basically = 996:
Rod your drain holes (or you can get OPC to)
Door membranes:
Not a 996 or 997, but this is basically what the membrane is/does:
Do this when any debris may be soft and moist (ie after extended rain, or at a pinch after a decent washing drench).
Use an airline to blow clear, or old springy type plastic coated curtain "rod" (net-curtain wire) - you want it firm enough to push, but flexible enough to go round radii and not puncture the drain tubes with sharp edges:
(remove the hook or eyes!!)
Access (rodding) may be easier via the lower exits.
This is illustrated in the diagrams and the photo of the wheel arch (behind wheel arch liner).
The exits you need to clear look like grommets.