Check the firewall rubber grommets that let the wires through from the engine bay into the cab also.

Mine ended up being the windshield. One area came unsealed. Had a windshield place pull it and reseal and no more problems

Same.

Thought I'd resurrect my own old thread to share findings in case it helped anyone else.

I had been parking in an underground garage from '20-23, and so I only ever drove in heavy enough rain a few times to get the windshield to leak. Last year I moved and parked outside on a slight incline with the nose of the truck downhill. This was the right circumstance to introduce the leak, which was due to an improperly installed replacement windshield.

Of course the replacement to fix it was also improperly installed and leaked from the OTHER corner. The technician returned twice to "fix it" which didn't, so I finally gave up and installed another brand new windshield.

That job's tech was able to point out where the other two had gone wrong. It's frustratingly simple, but the bead of adhesive has to be perfect before the glass is laid down or it won't seal.

My troubleshooting method was to park the truck with the nose slightly downhill and run an open garden hose on each top corner while i sat inside. I had the a-pillar trim removed to watch the inside of the top corners closely. I also had the kick panel trim removed and the carpet pulled back to view those areas but fortunately that proved to be unnecessary.

Water would enter in steady drips and run down the a-pillar toward the dash. It would find the firewall and turn down the kick panel (where lots of BCMs and fuses and relays are) and pool in the floor. Once that carpet pad is wet it will never full dry unless you pull it up and run a fan underneath. I have lots of practice doing that.

Anyway, all buttoned up now and watertight again. Hope this helps someone.

I get water on the passenger side floorboard. Of course when I'm ready to go after it with towels and the trim out, there's no leak. I also have a rear hatch leak but I bought a new seal ready to go. Both areas I messed with the seals when pulling trim to run amp and dash cam wiring so I'm chalking it up to my fault which is why i haven't gone in for warranty.

where did you run wires near the passenger side floorboard that could cause a leak? that insulation below the carpet is probably toast. I'd at least pull out all the insulation on that side if it's soaking through

I've dried it up each time so I'm hoping it's ok but I just ran amp wiring down the channel that's there with OEM wiring and the washer fluid hose. No cutting or drilling for anything there. Sunroof drains and condenser drains are clear. It's only the passenger side too.

that's interesting. hopefully it's not the windshield. besides the AC, sunroof and windshield I'm not sure what else could be causing a leak over there

So far no water up front and SoCal is getting a ton of rain (normal in rain states). The only thing I did was towel up the rear hatch and they are soaked at the end of the day. I wonder if this whole time water has been coming from the hatch and working it's way to the front but only the passenger side for some reason. These do sit butt high from the factory and I haven't lifted or leveled yet. When the rain clears I will change the hatch seal out.

Was the problematic replacement windshield originally installed by Safelite?

Unfortunately I don't know...I bought the truck with it. It was installed by "windshieldhub.com" and one of their subcontractors. I can say for sure it wasn't OEM.

The replacement's replacement isn't OEM either, and it has been great so far.

Watching this one because my 2020 4Runner proper stinks right now. It has been freezing here in the Philly metro lately so have not gotten to digging into the issue. At first I chalked it up to the dog in when wet but he has long since gone to the big doghouse in the sky and it has gotten worse so that can't be it. I have the kit to clean the evap coil but been too cold.

humans don't deserve the loyalty and companionship of dogs... if I could I'd adopt every dog in every shelter... but I digress

here are a couple ideas you could try to pinpoint the smell

- check the top of the carpet everywhere in the vehicle. under the seats, under your floor mats. anything wet? if so dig deeper, literally. pull up the carpet (can be done without removing seats, just remove some trim panels) and see if the jute backing / whatever insulation is there is wet

- if the carpet on the top is dry but there's still a stink then you have to pull up the carpet everywhere. if the backing is dry everywhere and the sheet metal floor is dry then it gets much harder

- usually the problem is AC related if you have smells when running the AC. if your vehicle is parked and you smell it as soon as you open the door it's probably not the AC

- aftermarket roof racks are common leak points, sunroof drains and AC line clogs and windshields. but those will show up as wet carpet/ floor boards. check rear hatch and drain holes in doors and rear hatch. run water through them to make sure there's no clogs in the drain holes

- when you find the leak and if it is the insulation backing on the carpet, don't bother trying to dry it. just rip it out. it separates very easily from the back of the carpet. just pull it out, throw it away, prop some wood 2x4 sections under the carpet and run a space heater for a day or so. that will dry the carpet. the top of the carpet will dry easily without the insulation backing. vinegar and water is great to disinfect as well

- baking soda will absorb any residual lingering smells, it works well and is cheap. if your vehicle is parked outside though and there's rain/mud from your shoes on the floor mats and you leave your rig parked for a few days and the weather is wet,damp and rainy, sometimes that inside air can get that stale smell. but it should go away rather quickly and shouldn't be that strong. this time of year/early spring when there's lots of rain and damp sometimes can make smells

Follow all the guidelines in T-SB-0094-21 "Odor Remediation After Water Intrusion" including pulling up the carpets as others have said.

After that, get some Mold Control (Mold Control Spray - Concrobium) available at any hardware store. Spray it on all surfaces you can get to.

Some people use an ozone generation, but remember that ozone is an oxidizer and may bleach carpets and seats.

If mold develops on the soft surfaces (carpet and seats), the "roots" will go deep and cannot be eliminated. In that case, replacement is the only option.

If you find moisture, a good dehumidifier may help.

good idea on that spray. I may have to make that part of my twice a year cleaning procedure lol. seems easy enough to just spray on and under the carpet , let it dry and maybe give it a wipe afterwards. I have floor liners but still dirt, water, mud, snow etc. always finds a way past them...