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I’m having a similar problem and can’t find anything in the internet that similar except your post. My 2016 keep Cherokee latitude has odd smell inside that’s pungent and strong. I looked around to find where it was coming from - in the spare wheel well to find lots of water. I’ve removed everything, including the plastic to pull the carpet up to dry everything out. It’s all dry now, including the thermal fabric on the right and left side. I sprayed the entire car with white vinegar to kill the mold and smell. The smell is returning... this past rain storm I discovered rain coming through the back right speaker holes. Was this similar to your situation? I ask because I’m unsure where it’s coming from. The ski racks looks and radio antenna appear sealed. I’m at a loss.
Were you able to find the source of this leak? I am experiencing the exact symptoms with my 2014 Cherokee that you described. This is a heavy leak that is pouring water out of the side panels below the speaker anytime it rains. I found about 4 gallons of standing water in my spare tire compartment (I have been ignoring the mildew smell for some time now and finally had some time to investigate). The roof rails appear to be water tight.
 

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Were you able to find the source of this leak? I am experiencing the exact symptoms with my 2014 Cherokee that you described. This is a heavy leak that is pouring water out of the side panels below the speaker anytime it rains. I found about 4 gallons of standing water in my spare tire compartment (I have been ignoring the mildew smell for some time now and finally had some time to investigate). The roof rails appear to be water tight.
Sounds like those pesky sealant cracks in the tailgate area. There's an active post about it going on right now. Known DEFECT...Open the gate, look at the drainage channel from the top, where the hinges are, and follow it down both sides...😎
 

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Welcome to the forum.
My 1979 Saab 900 had the perfect solution from the factory. Clever Swedes that they are.
Put a hole in the lowest part of the trunk and put in a rubber flapper valve that let water out and kept dust from coming in.
The REAL problem wasn't solved but at least you didn't have to carry around ballast.
There are flaps that let air out and don't let water enter on the left and right sides in the lower trunk area.
Remove the little cubbies on either side and you can see them. Make sure the flapper valves are ok.
Apparently you do not have a power lift gate.
If you do make sure recall R27 is done.
If you have a sun roof make sure the drain tubes are flowing freely.
 

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Mustangs and 'birds had those flaps from the factory (but my Escape didn't, and it was the worst for leaks), they should be in all ALL trunk wells!
 

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Were you able to find the source of this leak? I am experiencing the exact symptoms with my 2014 Cherokee that you described. This is a heavy leak that is pouring water out of the side panels below the speaker anytime it rains. I found about 4 gallons of standing water in my spare tire compartment (I have been ignoring the mildew smell for some time now and finally had some time to investigate). The roof rails appear to be water tight.
 

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It's one or both of your rear sunroof drain hoses! After wasting my time at a Jeep dealership who told me I had a welding structural problem I went to my old foreign auto mechanic that worked on my old VW. With the both back side paneling off, we pulled the inside roof down to find that the left drain hose from the sunroof had become detached. The hoses don't run the full distance from the sunroof to the wheel well where they drain. I'd say about 12 inches from the sunroof the rubber tube has a connection. Mine had separated which resulted in all the rain water flowing down into the wheel well. The mechanic dried it off, put a rubber glue around were the two tubes connect, and connected them. All is fixed and draining properly now. He said that happens because rubber shrinks over time due to extreme heat. The smell has gone away too which I'm relieved about. Let me know if you have more questions.
 

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Smart thinking. The Jeep you're referring to doesn't have a sunroof? If you say no I'm going to be confused about your water leak.
 

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It's one or both of your rear sunroof drain hoses! After wasting my time at a Jeep dealership who told me I had a welding structural problem I went to my old foreign auto mechanic that worked on my old VW. With the both back side paneling off, we pulled the inside roof down to find that the left drain hose from the sunroof had become detached. The hoses don't run the full distance from the sunroof to the wheel well where they drain. I'd say about 12 inches from the sunroof the rubber tube has a connection. Mine had separated which resulted in all the rain water flowing down into the wheel well. The mechanic dried it off, put a rubber glue around were the two tubes connect, and connected them. All is fixed and draining properly now. He said that happens because rubber shrinks over time due to extreme heat. The smell has gone away too which I'm relieved about. Let me know if you have more questions.
Thank you for the feedback. You were 100% right. Both of my rear moonroof drain lines were significantly restricted with grime/residue causing an overflow into the cargo area. I was able to clear the restriction by threading weed wacker line through the drain lines. Subsequently, I purged the lines with water and finally with compressed air. Now it is time to clear out the standing water and humidity....What a pain! Thanks everyone for the assistance.
 

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Thank you for the feedback. You were 100% right. Both of my rear moonroof drain lines were significantly restricted with grime/residue causing an overflow into the cargo area. I was able to clear the restriction by threading weed wacker line through the drain lines. Subsequently, I purged the lines with water and finally with compressed air. Now it is time to clear out the standing water and humidity....What a pain! Thanks everyone for the assistance.
Be careful with compressed air, you can blow the lines completely off, and then, you just thought the no drain problem was bad...😎
 
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If you used canned air with a fine straw and put the plastic straw down inside the hose, would that work safely?
Canned air like you use to clean a computer.
 

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If you used canned air with a fine straw and put the plastic straw down inside the hose, would that work safely?
Canned air like you use to clean a computer.
I guess that's better than the 100+psi from a standard compressor. I still probably wouldn't. Just proper preventative cleaning measures would alleviate the problem to even happen to begin with. Any sunroof requires preventative maintenance, to include greasing the rails, and other accessible moving parts, and cleaning of the whole mechanism, and drains...😎
 
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