Have you tried clearing your drains? They're located behind each seat under the plastic trays. They're small. Leaves and debris rinsed down off the roof easily block the hole, but once you locate them, they're easy to clear. Check out one of those helpful videos out there for a visual. If your drains get clogged, the water has only two places to go: towards the front down the interior wall behind your seat under all that plastic and under your carpet. The other is to the back, into your trunk.

 

Hi

I have had my MX5 RF from new. It is always garaged and never parked under trees but I have water/condensation in the boot and under the drivers seat. I have checked for blockages in the drains but cant seem to establish any. If I pour water down the drains it runs out the bottoms of the car (underneath). Do you know if this issue has been fixed by Mazda in the later models as I would like to buy a new one, however, if this issue has not been fixed I am reluctant. The dealer that I bought it from have been appalling with their after sales service on a number of issues. When I phoned them about this problem asking if it was a known issue, they said bring it in and we will look, but there will be a charge. They immediately told me that is was not covered under the extended warranty. I will not be purchasing my next vehicle from them.

 

open your trunk, direct a light stream of water down the trough at the back(behind the gasket). It flows down the sides right into the space at the top of the taillights ! If your taillight gaskets are bad (mine were) it just floods into the trunk. I happened to have a sheet of cork that I cut to about 4 ×12. I held it over the hole where the taillight goes. I took a sharpie inside the trunk and drew the inside hole on the back of the cork and the screw holes. Using an exacto knife I cut out the inside part,slipped the cork cutout over the back of the light assembly,over the screws and then reinstalled it. Tightened up the bolts(evenly)and bingo. No more leak. And a damn cheap fix. I'm so proud I saved $80 not buying a new trunk lid gasket.
Macman