I have a 99 integra, i just started getting water in my spare tire area. after i put my system in. i checked the drain tubes, there both in. i also checked the taillights the nuts were loose enough i could turn them with my hands. so i tighten them up. hasent rained yet so iunno if the problem is fixed yet.

 

Get some food coloring(make sure the color will stand out aginst your paint) and mix it in a bucket of water. Pour water over roof and hatch(mainly the sunroof and around the hatch weather stripping.) Pour a few buckets of this mixture over the car, wait a few minutes then look again. Hopefully your car isn't white with no clear coat......

 

weather stripping wears out man. could be something as dumb as the strip around the hatch isn't good any more and lets in some rain when you are driving/it is pouring out.
but that bucket idea is a good one. start with that.

good luck

 

The tail light gaskets usually cause this problem, it's fairly common. Either that or the sunroof drain