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Brought my sportrak two weeks ago and all has been ok till the rain started blasting down in the week and by friday I had over one inch of water swimming in the drivers foot well 
.Mopped all the water out with two rolls of kitchen towel and hair dryer on full to dry the carpet then shut myself in the sporty and had my daughter stick the hose pipe on to see just where it was coming in,at first I thought no problem its the windscreen leaking but under closer observation I bent my head up from the foot well to see under the dash and sore water streaming in from the main wiring loom gasket 
popped up the bonnet and located water passing the weather strip and dripping down onto the loom gasket,got her in the garage and got loads of rags to dry things of then put a good smear of clear silicon sealent along the inside of the strip and gasket,got the hose pipe out again and all is good :)no more water just a horrible damp smell that I need to get rid of.
News paper
Put loads of newspaper onto the floor. Its a good blotting paper.
I hope the wet floor is not also a result of a leaking heater matrix.
Re washing the carpets. It
Re washing the carpets.
It depends on what model you have, but the carpets in the post-facelift model seem to be of a far inferior quality of the original ones, and dont respond to washing very well (as I found out after a heater matrix adventure )leaving lots of creases which take about a year to go. No amount of me stretching and pulling them into shape seemed to have any effect.
I now tend to remove the seats (4 bolts each seat) and use the VAX machine with the small head which gives good results. They are also good insofar that any leak of water can initially be simply sucked out.
Dave with a Sporty
Dave with a Sporty
SMELLY CARPETS
I have a similar problem with one of my Sportraks but it is in the rear well and coming in from the rear roof joint if the wint is in a certain direction.
The best way to dry carpets is to take them out. It doesn't take that long and if you dont want to take the front seats out then using a sharp stanley knife cut round the brackets. The carpet will pull out from beneath the centre consol and goes back as easy. The carpet is clipped to the floor so it won't move about and can be removed easily in the future.
This will also allow you to wash the smell out of them and also to check the floor for damage and corrosion. I tend to leave mine to dry out in the air and also to check that the problem is cured 100%. It also save on the condensation in the car while they are driying out which can lead to mould growth etc.
The rubber grommets are usually fine unless not replaced correctly then they allow water to get in quite slowly over a long period or as in your case rapidly with severe weather. If you had been off roading in deep water you may have had the same problem but not with clean water(although the main loom grommet is high up so you may have been lucky).
OLDMINIMAN
M J Young