Sometimes rainwater can get in through the heater air intake. Check the drains from the heater plenum aren't blocked.
Air con systems can condense a lot of water out of the atmosphere when they are running, particularly in the summer. Warm air holds more moisture than cold air.
If you have a sun roof, the drain pipes from the channels it runs in may be blocked.
One car I had used to let a lot of rainwater in through a poorly fitting door seal, and one had a large grommet missing from the footwell, so a jet of water thrown up by the wheels got into the car.