It's wet on the underside of the rear quarter panel near where the ariel is.

 

That'll be it then.
With the roof down, have a look deep down in between the brushes where the roof motors are.
You'll see a plastic tray that catches water that runs off the soft top when it's up.
Theres a small hole that drains water, via a tube, out under the car.
Its like a large balck plastic drip tray one either side of the car.
Make sure the tube isn't blocked with leaves and stuff, if it overflows it runs down the inside of the qtr panel into the boot.
There should also be a rubber edge strip (like a 6" piece of wiper blade) to guide the water into it.
This wiper is glued to the metal of the inner qtr panel.
Both of mine had fallen off and dropped neatly into the drain holes

HTH
Steve.

 

My HT is on if that makes any difference...

 

Maybe not, as the drains are still used by the rubber window channels by the looks of things.
You see where the HT nicely mates into the rubber 'cup' on the car, at the back edge of the side windows?

Bit of a pain to see now though, it would have to come off.
ICBA to keep removing mine and I think it looks neat in place.

Hope you get to the bottom of it, its annoying!

 

I couldn't work out where you meant so I went with my original idea of the arial, took the base of the mast off the car and there is surface rust underneath so water has been getting under it, had to make a make-shift tool to remove it, put lots of sealant underneath and put it back, will have to see if it stops it.

 

One of the easiest ways to clear your drains is to get under the car, and VERY GENTLY feed an unfolded wire coat hanger into the drain valve, and up into the drain tube/tank. The valves are located Fwd of the rear wheels, as seen here:



If there is a blockage further up the line, you probably won't be able to clear it, so you'll need to remove the HT and have a dig around.

Steve - I've seen what happens to MX5s when the drains are neglected...it ain't pretty

Spies...even if this isn't the cause of your problem...it is still something I recommend everyone does at least 3 times per year.

 

I would be very surprised if it was the aerial seal leaking.
Have never heard of it, and the water does not puddle there.

 

Buy why would there be rust under the rubber if it wasn't letting water in?

 

surely a coat hanger up that rubber tube's a little aggressive?

I'm sure mine need unblocking but don't know where the water entry point is, i'm assuming at the far sides of the plastic tray the hood lives on when it's down

 

No, it really is fine, just be careful. The tube is very tough, so don't worry about puncturing it. Take extreme care not to dislodge the tube from the bottom of the drain bottle.

A compressed air gun works well, but will almost certainly leave a mess inside the cabin.

You can access the top of the drains from inside the car, near the seatbelt towers, as per m1bjr's post