When it rains, the floors in the car get wet and you can hear water under the trunk

you will have to look under the carpet and see if there are any holes in floor. there may be where plugs were that have come out and lost. you can get replacements at the auto parts stores fairly inexspensive.

check your trunk for water and if you can under back seat.i agree with hmac300 .is all of floor wet front to back.does carpet get wet while parked and raining or only while driving in rain