Anyone else have wet floorboards in a Cherokee after a rain?

Anyone locate the leak?

Have you had the windshield replaced?

Does it have a sunroof?

You pull the base trim off and roll back the carpet, then watch from the inside while another sprays with water hose in shower settle from outside car.  It's usually just door weatherstripping that is not as a good as new anymore.  You can replace, or try to reseal biggest problem areas with clear silicone and drill a 1/8" hole in floorplan at lowest point so it can drain better.

Both sides or one side and if so, driver or passenger?

Make sure the Condensate drain for the defrost/A/C isn't plugged.

I had the same problem with my 2008 Patriot. Turns out it was one of the sunroof compartment drains. It got plugged and rain coming past the gasket would end up on the passenger side, under the front seat. Judicious application of a little compressed air made things right again.

I haven't replaced the windshield.  

It's the driver's side.

A/C box drains.

Cowl drains.

No sunroof.

I pulled the carpet back some.  dried the puddles with a towel.  The insulation under the carpet is...unfortunate.  I pushed it up as much as I could.  I recon the shell unibody comes down the line at the factory and that underlayment goes down first.  It has pass-thru holes in it for various things.  

I pulled the wiper arms and got the cowl cover off.  I laid a water hose in it and went inside to look.  I saw water trickling , but I'm not sure it wasn't wringing out of the underlayment as I folded it and pushed it up to get a better look.

I looked inside the cowl.  I saw where that seam-sealer putty, at the very far right, and almost not visible, didn't bridge between what might be the sheets of a welded pinch seam.  Couldn't tell, but don't see why the putty would be there unless there's a seam.  The putty dries like hard plastic but I could poke my finger under it.  I bought some sealant at Autozone and very liberally applied it.  It was one of those situations where you could see the gap to be sealed until you put your hand in the only way it could go.  Spread it by feel with my finger.  

If cussin' fixes leaks I expect success.

I've only just now had a chance to check whether the putty application fixed the leak.  It did!