Why is water leaking into trunk?

Hunting water leaks is a pain in the tailbone job to do. I'm assuming yours has the jack in the floor of the trunk, under the carpet.
The spare wheel well is the lowest point in the trunk so the water will collect there regardless of where the leak is. Start with the simplest tools, a flash light and the palm of your hand.
How much water is collecting and how fast does it fill up? Rain water coming up through the floor is unlikely unless the floor is damaged.
First take everything out of the trunk that wasn't in there when it came out of the factory. Take a really good look at the carpet and trunk side liners. Use the palm of your hand and feel the floor carpet for wetness. Your feeling to see if it is wet in a particular area. Using the flashlight look for darker patches as carpets often darken in color when wet. Move to the rear of the trunk and feel the liner on the back of the rear seats. Next run your hand over the side panels where the wheel arches are. This will give you clues as to where the leak is possibly coming from.
If the whole trunk carpet and liners are bone dry the leak is from under the car.
All the doors, the trunk lid and the sun roof are fitted with rubber seals to stop rain and road splashes getting inside the vehicle. Over time these perish and start to leak. Run your hand around the underside of the rubber seal the trunk lid sits on when closed. This is the most obvious place it will leak from. You can do this on each door as well because water can travel a large distance before it finds somewhere to create a puddle. A Sunroof can also leak but they tend to cause puddles in the foot well.
If you get a few dry days you can test for leaks with a hose pipe. Keep the trunk closed and make sure the inside of it is totally dry. Remove any spray nozzle from the hose so it flows at regular pressure. Carefully aim the water so it only flows over the trunk lid. Let it flow for a minute or two trying not to soak the doors at the same time. Turn off the water and leave the car alone for about 10 minutes. Wipe off any excess water on the trunk lid, open it and see if its now wet inside the trunk. Yes? the trunk seal is leaking. You can use this method for the doors and sun roof as well. Door and trunk seals are usually just a 'Push on/Pull off' fit so you can easily change them yourself.

Usually the leak is from a faulty gasket, or the lid is not adjusted correctly to seal against the gasket.

check the gasket inside your trunk, were it meets your trunk lid first, then if thats ok, pull your spare tire out and make sure the drain holes have the rubber plugs in them, if you have had an accident and it was in the rear end area, bring it back to the shop that fixed it oh one more thing, your trunk lid might need to be adjusted, check to see if it lines up, if the gaps around it are all the same, if not, not to adjust it,

see if you can slip a dollar bill in anywhere around the trunk lid with it closed. or get in the trunk with someone running a hose that can also let you out when you are done

The green solution is Radiator Fluid. There is a leak from the Heating / AC somewhere. Since you have already checked the Heater Core then the likely culprit is a loose, cracked, connection or hose or line that has a hole. And because of the heat generated, they are hard to detect because the leak "dries-up" before you can detect "where".
Because of this: re-expose the Heating / AC system again = take the dash components back off. You can reconnect the electrical components that turn-on and run your heating controls. Use dry, white paper towels wrapped completely (from one end to the other end) around the hoses/lines. Start you car and run the Heating. The paper towels will not dry as rapidly as the lines will. The wet towel section is the culprit and the one that needs to be replaced.
Let me know if this helped, or if you have additional information or questions. Feel free to contact me at FixYa.com!

The two main causes are: 1) the rubber seal on the body where the trunk lid closes. check for tears or where it is not seated properly
2) The rear window is leaking around the seal
Of course if you have an antenna or the like which has been mounted on the rear fenders that seal could be the problem.

Here is the best way to find out where the water is coming in. Get inside the trunk and have someone you trust close the trunk. make sure you do it when it is daylight or a well lit garage. while you are in the trunk with the lid closed you will be able to see light where there is any gap around the trunk seal and that will be where the water is coming in. some times the sides of the trunk opening gets bent down causing the trunk gasket not to seal properly.

Sounds to me like your issue is with condensation from your air conditioner. The condensation isn't properly draining, probably from a damaged or clogged drain hose.

check your heater core they tend to leak..