Look at the rubber seal which will either be on the trunk lid or the lip of the trunk and see if it is still soft to touch, complete and shows no tears. Also look to make sure that there are no leaves or other kind of dirt that would stop rain water from flowing around the outside of the seal.
Look and see if you have a Radio antenna coming into your trunk. The Rubber seal at the bottom of it may be worn out. Check to see if the antenna is loose to your touch, it may just need tightened up.
Some spare tires are held down by a bolt that goes through the body of the car. Without the bolt, water can seep in if you drive through lots of rivers / puddles.
Some Taillights actually form a seal around the outside of the trunk and if the lights are not secure (they move), the rubber seals around them are dried out or the lens of the lights are cracked, broken or missing then that can cause leaks.
Is your lock or handle secure on your trunk? A bad rubber seal here will let water in.