Bought my latest SE when I was on a contract in Lincolnshire and parked it in my hotel car park for a couple of months. Thought I'd bought a mobile swimming pool for a while till I understood what was happening. Car park had a slope and park one way the footwells would fill, park it the other way and the hollows behind the seats would fill. I even bought a rechargeable wet/dry hand held vacuum cleaner to get it out!
I found rain falling on the door windows will get inside the door, unless the outside rubbers are really new and flexible, which most aren't. No problem as there are drain holes in the bottom of the door, hidden by the door card, that lets it run onto the plastic door sill cover that has a lip on the inside edge to stop it coming inwards. The door seals should have a couple of hard rubber 'pips' along the bottom edge so they don't trap water on the sills and thus it flows to outside. If they do trap water it flows inside as the only way of escape.
I noticed that after heavy rain, when I opened the door the sill was covered in a lot of water that would flow off the sill onto the ground, and often as not I had a wet carpet. My 'pips' were missing so I scrounged some yellow/green earth sleeve and insulating tape and added 3 'drain tubes', front, rear and middle each side, that go from the top of the plastic sill cover down past the door seal as a temporary fix. Problem solved. Not sure if water flows in the tube or it just holds the seal away to let water past but it worked.
3 years later I'm still relying on them, (If it ain't broke, don't fix it...

), but have to renew occasionally. In the photo the middle one has dropped off.
tubes.JPG
It looks from your photo that you've removed the plastic door sills while investigating your problem so have created a problem in itself...
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