Had water in trunk, actually spare tire well. Took liners off and crawled in trunk while daughter sprayed water. Such a simple fix! Must have over stuffed the trunk at some point and popped out a fitting for the parking brake cable. Water coming in from drivers rear wheel well. Can be fixed by following cable behind rear drivers side tire, take off one hand tight bold to reach behind the

Drivers side wheel well leak.

Fixed plastic piece snapped back in place

Drivers side rear wheel well. Cable. Small bold that is hand tight, remove to access from outside.
trim. Reach up and snap an oval piece of plastic back in place. 5 min job.

 

Hello,
My car is a 2014 Mazda 3 saloon 2.2l diesel.
If your reading this you have probably experienced the same problem I have as I have just found a pool of stagnant water in the trunk spare tire well, about an inch deep. There was a layer of felt material here which was glued to the bottom of the wheel well and this was just completely soaked through and lifted up no problem. As the water was stagnant I just threw this felt out and drained the water out through the black rubber stoppers in the bottom of the well, there are two of them and are easily removed and returned to position. I completely dryed out the area and lifted out all the floor liners and the dark grey foam which i use for holding my tool case and car jack. I also removed the hard plastic cowling which spans the bottom inside lip of the trunk which surrounds the latch hook loop, there are two screws which hold this and when screws are removed you can pull this section off by pulling up firmly but carefully at either end as its still held in by clips. Once this was all done and all dried out most of the painted trunk floor was now exposed and I dusted some talc powder into the whole area. As i live in Ireland It helpfully rained again overnight though you could just use a hose and spray the car for a while. On opening up the next morning I discovered that my leak was coming from the inside bottom edge of where the trunk seal gasket is though I had suspected that the seal glue holding the rubber gasket to the body might not have been glued correctly at at least two points as lightly pulling up the gasket with my hand along the full length revealed that it was no longer attached at these areas. I removed the rubber seal gasket completely and it was apparent instantly that there was some wettness and a little rust on the bottom inside edge of the trunk edge. After I cleaned and dryed all the adhesive off the inside edge of the trunk I set about removing all the old adhesive from the inside of the old gasket..(Now I understand you may be able to order a new gasket from mazda which has the silicone/adhesive prefilled..though not sure of this!) The black rubber gasket inside channel can be easily opened up by approx 1cm along its length by prying a little using your hands as it has a bendable wire/strip on either edge of its opening, I then carefully used a flat head screwdriver to remove and scrape all the old white silicone adhesive without puncturing the rubber. I also had a large bucket of hot-warm soapy water to hand which i bathed the gasket in as I did this. I also used an old rag with some white spirit on it to remove any remaining silicone. After drying the rubber gasket fully I used a tube of grey Tec 7 to fill the length of it with an aplicator gun which is a strong adhesive but also remains flexible and waterproof so should be a better material than that used by Mazda. As I filled the gasket I closed it with my hand with only a little force needed to reclose it. I then reattached the gasket to the car trunk edge pushing down hard along the full length and closing the trunk to maintain force as it dried. All trunk liner and covers returned to place after the job.
It's been over a week since I have done this and there have been some very wet days here since and so far the trunk has remained completely dry.
There no doubt could also be some other ways in which water could make its way into your car..thinking backlight seals or from cable routes perhaps as others have suggested.

Inside edge of truck body under rubber gasket where you can see some of the old rust, wettness and an area opening which i filled with a little body filler..

Other area along bottom edge where rust can be seen with opening

Inside edge where you can see water ingress


This is the tube of Tec 7, I used grey though it also comes in black. It is adhesive but remains flexible and waterproof so should prove to be better than the original material used by Mazda

 

Nice posting I enjoyed reading

 

I had a 1998 Protege that was in an accident. A month or so after it was repaired, I noticed the spare tire well had water in it. I drained it and sprayed water on the underside near the trunk and I could see the water coming in. I called my insurance adjuster and they had somebody put weld over the spot and it never leaked again...