Why does the car smell bad when it rains?

i would pull everything up in the hatch and check for leaks

 

Is this a relative new problem or one that has plagued you since new? Does it affect a specific area or does it seem to be concentrated in one area? Before pulling up everything in a specific area and checking for leaks there, this information will help us to give more helpful information.

 

Do you use the AC a lot? Relentless use can lead to mildew.

 

I had a similar problem and fixed it by running ac(to wrung out humidity) and keeping fan mode in non-recirculate(to stop humidity buildup).
Humidity causes mold. And removing humidity dries off the mold.

 

Im not sure how this model is but I know the get 2 used to have a issue sometimes where the water would get below the battery area because of a very small crack in the roof and hatch area. I normally clean the hatch and get some flex seal. And spray iron the passenger side of the hatch, all the way up to the small crack area on the roof.

 

Is it a mildew smell? Water left on the A/C coils can mildew which can stink. If you don't have a carbon-activated cabin air filter, get the FD157 (Fun Driving) filters on Amazon. ($15 for two) I replace ours yearly and haven't gotten any bad smells.
Another tip that helps with the smell is to run your fan on HIGH but with the A/C turned off for about 5 minutes whenever you are done driving the car for the day. This helps dry out the water that's on the coils and vents to prevent mold and mildew.

 

Have you tried replacing the cabin air filter?