There's a deep well outboard of each seatbelt tower. In the bottom is a
drain that dumps in front of the rear wheel, through a rubber flapper.
The drain's job is to carry away water that falls on the roof (hood),
collects in the rain rail, and runs into the wells. If the drain is
clogged, water backs up and does what you describe. A broken rain rail
will do the same thing, but that's less likely unless the roof was
inexpertly replaced.

Reach down the well and remove any dead leaves, etc., that you find. If
you pour water into the well, it should immediately drain under the car;
if it doesn't, poke something--gently!--into the drain to clear it.

Drain cloggage is minimized by using the boot cover faithfully.