It is probably the drain holes block with crud in the bulkhead. You will need to take the cover off at the rear of the engine bay (if you have one?) and you may well find the water is even sloshing around in there. There are two holes I think, at least one is situated under the battery so that will need to come out too.
Thats the most likely culprit, but it could be windscreen seal, or even a sunroof seal if you are lucky enough to have one.