The water might be leaking in at the rusty spots... But at least for the newer cars that I own, the taillight gaskets are popular leaks, too. Take off the taillights & check the gaskets. If the car's ever had a collision, maybe the trunklid gasket doesn't fit right?

You could crawl into the trunk with a flashlight, then have somebody hose down the car.

Or you could wait till it's dry, put talcum powder all around inside, then hose it down. Water leaks will leave tracks in the powder.