The windshield might be leaking. Have you ever had the windshield replaced? The gasket might not have been installed correctly. Or even if original to the car, the neoprene surrounding the edge of the windshield may have cracked. You may need to have the windshield removed and neoprene gasket replaced. This might be covered by you comprehensive insurance, so check.
It could also be rain coming in through the air venting system. Sometimes leaves, sticks, spiders, etc can clog this up. Especially consider this if you routinely park under trees.