My 2003 Civic did the same thing if there was a heavy rain or after going through a car wash. I found some water leaking out of the air outlet that points towards your feet on the driver side. Not sure if this was ultimate fix but i replaced the foam seals on the RH lower windshield plastic cover that is directly above the outside air intake and where cabin filter is. Air or rain water should only come in on from the vents on the driver side. The plastic panel was bowed slightly from age and rubber was also smashed not making a good seal. I ended up using a thicker foam strip with adhesive backing from auto parts store, a replacement from Honda is probably way more expensive but would fit better. So far no more leaks.
Driver side floor soaked when it rains....
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Just to make sure we necro this old thread properly(any action is good action 
)
I would add that if you have a sunroof there is a gutter drain tube behind the side panels under the dash that has a little rubber 90degree elbow that gets popped loose sometimes. Wet stinky carpet results.
) I would add that if you have a sunroof there is a gutter drain tube behind the side panels under the dash that has a little rubber 90degree elbow that gets popped loose sometimes. Wet stinky carpet results.
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