My '04 BMW 330cic has water in the spare tile well after every time it rains, but the rubber trunk seal looks secure and the upper part of the inner trunk is not wet. Any ideas on how the water is getting in?

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.

Check the Rubber sealer. The rubber that goes around the trunk it should seal it if not you would need to change it. Those parts deteriorate fast depending on the weather region.

that be hands on checks. sure whole
my wild guess...
1: bad seal
2: collision damage not fixe
3: a cocroach that die in the upper part of seal (look)

It is most likely the boot rubber seal there is commonly two rubbers that adjusts the boot close height see if you can turn the right hand adjuster in to make a firmer seal. Also check that the seal is not pinched and is located properly. After market rubber is not expensive if you want to try to replace the whole seal.

sounds to me that the rubber seal for your trunk needs repaired or replaced

Hello and welcome to FixYa!

As a first course of action, I strongly suggest that you replace the weather rubber strip of the trunk. If the rubber is worn out or not properly secured, the water tends to leak inside. Have it secured and replaced then observe how it goes.

Hope this helps and thank you for using FixYa! Have a good one!

It's most likely the weather stripping along the top of your trunk, where the hinges are. There is probably a bad contact, or missing the weather stripping.

pour a small amount of water down the back of the car, give it some time and then take a look inside maybe you will see where it's dripping from. if you can, fold your seats down and sit inside the car with a flashlight while someone else empties a glass of water approx. on your back window, roof of car etc.

Hope this helps :)

The majority of cars like these have a small dollar coin size piece of foam/rubber that plugs a drain hole. It may have been put on at the factory with some type of glue/adhesive so it may not be the easiest thing to take out. You may have to take out the spare tire (not sure on this car). You may want to try and re-do the foam/rubber stripping around the seals of the trunk. It is not the hardest thing in the world to do (in order to stop the water altogether)..

I'm assuming you checked the seal around the trunk just to make sure it wasn't bumped off track in any way maybe taking groceries out or putting anything in? The car is too new to be suffering from any dry rot I should think. If you drain the water and it comes back I would think the seal around the trunk would be suspect in the matter.

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.