I had the same problem in my 2011 SRX. Common problem is the sunroof drain - the hose is too short and it vibrates out. Your dealer will know about it - insist they pay for it even if out of warranty.
If you are handy, this is easy to check (but hard to fix) - pop off the interior panel on the front A-pillar (the A-Pillar is the post between the windshield and the door). You can pry it off with your hands, no tools needed. After it is off you will see some wires and a white plastic tube about 1/2" diameter. That white tube runs from the sunroof drain channel in the roof (one of several) down the A-pillar into the firewall just below the dashboard at the very bottom corner of the windshield. It has a black rubber fitting that fits into a hole in the firewall and that is what pops out. So when it rains, the water runs down the top of the glove box, drips on the carpet in the passenger footwell. This is a big issue as it runs right over the electronics and the ECM - this will cause BIG problems if not fixed (aside from the inevitable damp stink).
If you use a flashlight and peer from the outside of the car in the corner of the windshield on top of the dash you can see how it connects (you must remove the A pillar cover first). It is extremely difficult (impossible) to use your hands and pop the fitting back into the firewall. You can either disassemble the dash or like I did make a long bent special tool to push the black boot/tube back in. Tip - use some dish soap as a lubricant.
To test the if this is your problem just tape the entire sunroof gap from glass to roof all around to seal it. Hose the car and if the problem is gone, you found your problem.
THIS WAS VERY HELPFUL. I HAD BEEN HAVING A LEAK IN MY 2010 SRX FOR ABOUT 3 WEEKS AND HAD NO IDEA WHERE THE WATER WAS COMING FROM UNTIL I READ THIS. SURE ENOUGH, IT WAS THE DRAIN HOSE, IT CAME LOOSE AT THE TOP. IT TOOK A LITTLE WHILE TO FIGURE OUT, BUT I WAS ABLE TO CONNECT THE HOSE BACK AND YES IT IS A VERY VERY TIGHT SPACE. BUT THANKS TO YOUR HELP, I FIXED IT; AND I'M A WOMAN. LOL.
I have a 2012 model, and starting having this issue. What I found was similar, but not the same. I had water dripping down onto the passenger floor. Didn't notice it until we got weather tech floor mats. So, took out the glove box and pulled the fresh air filter, and the housing had water in it. Pulled the cowl panel and looked down. The water than drains out of the sunroof drops down onto a panel. It should keep running straight down, but some water follows the gap between panels, carries over to the fresh air intake, then drops into the hvac system.
To fix this, I did two things. I silicone in the gap after the last drop out (there are three notches that should let water run down the panel and away from the hvac). Then, I installed a longer tube that directed the water run off over the panel so no water gets back onto the panel and runs over to the hvac.