Start with a garden hose to lightly water the trunk lid, wait for the water to mostly run off, then open it and check on the rubber weather strip for wet spots. If you find evidence there of water sneaking in, you can sometimes bend the pinch weld that weatherstrip clips onto or is glued to so it will seal better. If no water comes in with a light hosing, look for debris buildup in the drain channels that is slowing how quickly the water can run away. It may be building up until it's high enough to sneak over or under a seal.
Try to determine the area of the leak by where the water is pooling. For example, if you're finding it behind the right rear wheel but not in the middle, you know it's not leaking in from the left side.
There are powders made for checking how well rubber seals are sealing. You might also be able to crawl inside, close the lid, and see where light shines in. (It's rather convenient to have a friend along who will let you out)!
If you have a sun roof, they have drain tubes that can become plugged with debris. A disconnected drain hose can allow water to run into the trunk too.