Start with the holes where the drain pipes go down through the floor to the tanks. Usually they are much larger than the pipe to make it "easier" for the folks to put things together at the factory.
Next, the rear hatch door if you have one, think you do. They generally seal poorly, just enough to accidentally keep water out. So dust will easily get through the poor seal. If the seal is worn and permanently compressed you can replace the seal. One thing I've done is put a small "D" seal on the surface that the seal mates against to help fill gaps in the space, so you have 2 seals meeting each other. You can use "D" window seal avsilable at hardware store for this or order from places like OODM or VTS.