I drive 600 miles a week in my 2002 GT TDi 150bhp and recently, the floods and rain led to my footwell on drivers side front and rear having water in. I have a sunroof so that was my initial idea but after 2 weeks being sealed with tape, water still got in. After several wild goose chases, I finally checked the rubber nipples that sit in the door frame - as soon as I squeezed the driver door one with thumb and forefinger - a torrent spewed out despite no rain for 2 days! The rear door one also was full. Over time they had just got blocked.
I have a tool for cleaning my camel-back water bottle which is basically a thin brush on 1 metre of flexible cable - I fed it up the nipple and it had a huge effect bringing out tons of shi*! Since then - more rain but no more damp carpet.