MX5s suffer from rust in areas that cause MOT failures.
Typically, MX5 Mk1, Mk2 and Mk2.5 suffer rust attacks to the rear sill and wheel arches areas. It usually shows on the outer sill or around the wheel arch ie the bit you can see.
Mk2 and Mk2.5 also suffer rusting from front chassis rails.Until fairly recently this hadn't been picked up during MOT testing. In the last few years testers have been checking these rails.
The MK3 and later cars aren't suffering in the same way as earlier models at the moment. But the rear of the car was poorly protected when it left the factory so we should expect Mk3s to require welding work soon.
The above picture shows an outer sill replacement in progress. The rusty metal been removed so that new metal can be welded in. This car has almost perfect re-inforcement panel, so that doesn't need replacing.
The picture below shows a whole wheel arch replacement before welding. This is one of the two ways a wheel arch can be repaired.
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We would need to see you car or at least some pictures to give you some idea of the work that is needed.