1 - Water in car gets trapped

Rain Water is drained through the car frame on some convertibles.

Sun Roof drain can get blocked.

Whenever you use your AC, condensation forms on the equipment and this has to be drained out. One nice mechanic had put a piece of foil in the AC drain of a car we worked on. Simple fix to remove but it had annoyed the owner for several months.

External Vent for your car's Driver / Passenger Heat / AC has a drain and when this gets clogged the water will spill over into the intakes. Common problem as leaves and other debris collect in it.

2 - Car Design Flaw

All cars have a external vent intake. Some Chryslers have been known to have an issue during heavy rain of water coming into the passenger side. From what we have seen, this is caused by rain splashing into the trough below the external vent and the rain then splashes into the bulkhead of the car. 

3 - Bad Assembly

Eastern Block cars from the days of the USSR had some dubious water proofing

4 - Bad Repair

Maybe a seal was not replaced, weld not done correctly or a hole sealed that should not have been. Can be very tough to diagnose.

5 - Part Failure

Water in car can be caused by rubber seals that dry out / break as they age and no longer stop the water. Cars over 10 years are very prone for this.

Heater in the car can crack / rust out and leak coolant into the inside of the vehicle. Very easy to tell by its smell and lack of coolant in the radiator.

6 - Water in Car due to Part Removal

Once had a suburban 4x4 where the driver complained that water was coming in the overhead console. It turned out that the roof mounted telephone antenna had been removed. No-one at the dealership plugged the hole.

Radio antennas are the most common issue with this as they can be mounted so that they are actually penetrating the waterproof outer skin of the car. When removed they leave a hole that allows water into places where it is not supposed to be

7 - Extreme Environment

Snow all over a car can put water where the designers never dreamed it could go.

Flooding can exceed the vehicles water proofing level.