It's early (relatively) here and I haven't had much coffee yet but I'll venture a guess.
Roll up the windows!
JK. If you are referring to the basement compartments just behind the wheels, check a couple of things.
1. compartment weatherstripping
2. compartment latch alignment and pressure against the above meantioned weatherstripping
3. rear of wheel well re: gaps in foam/rubber insulation.
Check #3 with a garden hose with the compartment door open (watch your head) and see if you can spot leaks. It may be coming from somewhere else and traveling so look UP inside the compartments for staining or drip marks.
If the insulation/undercoating has gaps/cracks, fill them with a comparable product and test again.