Water Intrusion - how to investigate

First off — really glad to have found this forum!
New reader and first-time poster here. I recently discovered the infamous AC drain clog issue and plan to check that today or tomorrow just to rule it out as a suspect.

For context:
  • I’m not hearing any sloshing during turns.
  • I think I remember seeing it drain before, but I park on gravel, so it’s hard to tell if there’s usually a puddle.
  • I do use auto circulate and often let the car idle with AC on (newborn + heat = survival mode on pediatrician trips 😅).

What happened:​

After a massive rainstorm, I vacuumed about 4 gallons of water out of the passenger floorboard, under the seat, and even a bit from the rear (less back there).

A small water stain on the C-pillar that had been there for months suddenly expanded from 1 inch to about 10 inches. That was my first clue something serious was going on.

What I’ve done so far:​

  • Cleared the passenger-side sunroof drain.
  • Didn’t tackle the rear drains (not ready to pull the headliner).
  • Found a huge amount of debris behind the passenger wheel well — years of leaves and dirt from the previous owner, which likely caused backflow.

Thought that fixed it...


Two weeks later​


Another rainstorm hit. The passenger floorboard was wet again. Not flooded like before, but definitely damp — especially in the front. When I open the VIN door, I can feel moisture and the carpet is damp again.


The C-pillar stain hasn’t grown, which is interesting — that’s what kicked off this whole investigation in the first place.



Theories​

  • If the sunroof drain is clear and the C-pillar hasn’t leaked again…
  • But I’m still getting moisture on the floor…
    Could it actually be the AC drain?
    Or possibly the windshield or sunroof seal?

For what it’s worth, the AC does smell, which makes me even more curious to inspect that drain line — maybe both were clogged, and I only fixed one of them.



Appreciate any insight. I really hoped clearing that sunroof drain and cleaning the wheel well debris would solve it, but looks like there’s more digging to do. The C-pillar water ring still concerns me most since it suggests water intrusion from above, not below.

Thanks in advance for any ideas — this has been a headache, and I’d love to finally get it fixed once and for all!
 
Can you pour some water on your windshield to do a seal test?
Certainly worth a try - where would it exit if this is the entry point? That way when I set a hose on it I can gauge if it’s making its way into the cabin. Suppose really anywhere at the top where I suspect it starts. The soft foam piece behind the styrofoam was saturated when I had it exposed two weeks ago to vacuum and can start watching there?
 
Wanted to comment here; This is something I've been thinking about regarding my CX-9. I see a design issue with the way there is no way to clean the debris that accumulates through the windshield wiper holes (where the wiper arms attach to the motor points). They allow for leaves to fall under the front vent cowling and there is NO way to clean these aside from pulling apart the long plastic piece that extends just below the windshield. This is something I've been meaning to do just do see how much stuff is in there, possibly accumulating in the venting and drainage systems, possibly leading to water backing-up and leaking into the passenger area. Has anyone else felt this as a concern with that design? Thanks.
 
Wanted to comment here; This is something I've been thinking about regarding my CX-9. I see a design issue with the way there is no way to clean the debris that accumulates through the windshield wiper holes (where the wiper arms attach to the motor points). They allow for leaves to fall under the front vent cowling and there is NO way to clean these aside from pulling apart the long plastic piece that extends just below the windshield. This is something I've been meaning to do just do see how much stuff is in there, possibly accumulating in the venting and drainage systems, possibly leading to water backing-up and leaking into the passenger area. Has anyone else felt this as a concern with that design? Thanks.
I’ve wanted to pull that apart and see for myself. With a newborn and house projects trumping my work on vehicle, I’ve sadly not been able to tackle it.

Ac drain for me wasn’t clogged. So, cleared wheel well debris which was blocking the exit path of the sunroof drain.. confirmed ac is draining properly. Now not sure what’s next lol maybe that cowl section.

We’ve been lucky in SE Virginia with little rain last week or two. One storm I checked following and the bottom of carpet was damp. Not sure if it was residual from the 4 gallons I vacuumed out the week prior.. dried it best I could but wouldn’t be surprised if I only got 85%.. what a mess lol not been fun and can’t afford a mechanic to investigate right now let alone the time to go drop it off etc with needing to stay home with a 7 week old to support my wife as she recovers.
 
I see a design issue with the way there is no way to clean the debris that accumulates through the windshield wiper holes (where the wiper arms attach to the motor points).
Do a search for "windscreen wiper cover dust proof protection" on Amazon.
 
For your information: I cut the hole in the silicone cover "plates" a little bit larger to make them fit better around the wiper shafts of my CX-5. YMMV.
 
Nice, those are cheap - for the security of it potentially being a thing.. doesn't hurt to grab.

Still investigating. May try to shove a carpet fan back in there to dry again and see if it comes back or if it was residual.

The C pillar stain if parked a certain way is what I wonder about. When backed in, i think the water moved to the rear outlet, which could also be clogged.

Really don't want to pull headliner if I am not certain it is it xD

Ahh... never again on a sunroof. Knew i was taking the risk.. gambled since every other aspect of the vehicle was cleaaaaaan.
 
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