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Examine the door and trunk rubber seal to determine if they are damaged. If so, install replacements.
It may also be the "rain rail". This is a piece of flexible plastic. It is attached to the rear trailing edge of the soft top, and then bolted against the body with spreader bars. You can see it if you remove the rear deck carpet.

The purpose of the rain rail is to collect water running down the back of the top, and channel it to drain tubes that empty to the ground just behind the doors. With time the plastic becomes brittle and cracks. If it leaks, water will drain onto the rear deck below the carpet, and from there into the trunk. Remove the rear deck carpeting and check the padding below. If it is wet, that is the cause. Without removing the carpet, if the car smells "damp" inside, there is a good chance this is the cause.

Replacement rain rails are available from Moss Motors (miatamania.com). Changing them is not too difficult. You have to unbolt and remove the entire top with frame (which is much easier than removing and reinstalling the top on the frame). Then drill out the rivets holding the old rain rail, and install the new one with new pop rivets. I wrote the original question. After hearing about problems with seals around tail lights in '90-91 Miatas often being the problem, I got a tube of gasket seal, and filled in gaps at top of taillights (with trunk lid open); it dried to look like it came that way from the factory, and I've never had a problem since. I was getting buckets of water before.

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Q: How can you stop rain leaks in a '91 Miata It gets in the trunk and in the passenger and driver compartments; tried cleaning out the drain holes under doors to no avail.?
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