Water on right side of trunk and spare tire well in my 2006 honda civic

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.

try looking at the trunk gasket! if its bad it will let water leak in the trunk as well

I am assuming the water comes in when it rains.
Could be the trunk gasket or the tail light.
You may need a body shop to find the leak.

its along way from the trunk to the back seat. check the back window,and the doors, get a water hose and have someone inside check it for a leak. Water in the trunk is usually caused by bad seals at the tail lights. But water in the trunk usually stays in the trunk and spare tire area. If the car has been wrecked, then who knows.

Probably the quarter light window (triangular) behind the rear passengers door. In daylight sit inside and get someone with a hose to spray lots of water in that area. If you see any water in the inside try to trace to source. If you can look in the trunk with it closed try the same to look for where the water is coming from. Otherwise sit in the closed trunk with a torch and do the same. Just make sure your mate lets you out then shout him or her a beer. :-)

Check the trunk rubber for damage and/or improper mounting. There will ordinarily be drain holes in the area where the tail light assemblies mount to the back of the car. If they are plugged up, the water will have nowhere to go when it rains, and will seep through the gasket between the tail light housings and the body metal. If unable to find the problem, have someone soak the back of the car in the trunk / tail light area with a garden hose, and watch for water intrusion from inside the trunk with a flashlight (hopefully, the rear seat backs flip down so you can gain access to the trunk from inside the car). Good luck!

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.

http://www.in.honda.com/Rjanisis/pubs/SB/A92-050.PDF

Mother nature is too slow in finding leaks. Have someone small get in the trunk with a flashligh and watch as you run a hose over everything. LET THE PERSON OUT!

The rear window seal may be leaking into the trunk.The window may need to removed to fix it correctly then you can see if there is rust holes in that area.