How does water collect in the trunk spare tire tub? The hatch rubber looks good. on 1994 Chrysler LHS

I used a shop vac to get it out then 1 week later a musty odor developed. I'm puzzled how the odor seems to come from the HVAC system vents. I've only had this car since Feb 2011 so I don't know if the water continues to accumulate. Is there a way to drill a hole for drainage without it then letting in road water from below and/or exhaust, or is replacing the trunk rubber the proper solution? Could there be two separate issues (trunk lid leak & HVAC mold)?

Asked by for the 1994 Chrysler LHS
rear window may be leaking.

Thanks for your response. How would you suggest I determine the source? Could I run a low volume water hose over the trunk lid seals first & if no pool of water collects in the tub then proceed to the rear window?
thats exactly what we do. somebody in trunk with a light and hose it off.

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On any car, water in the trunk can be caused by a broken seal around one or both of the tail-light assemblies. The assemblies would have to be removed, the old seal scraped away and a new seal installed. Hope that helps. - Good luck.
Thanks for your input.