Mine is a 5-spd GS as well (no vtec...). How many miles do you have on yours? This one recently topped the 200k mark, but it runs better than my f-150 (@~145k miles)... and my f-150 runs well. It rained today, and when I hopped in it, there was more water in it (different leak... probably sunroof this time). ugh. I'm falling in love with the car, though.
I am at the 238,000 mile mark. This is on the original engine and transmission. The main thing to keep maintenanced is the timing belt. If you don't know when it was changed last it would be a good idea to change it and the water pump together. Where is the water in your car? The passenger floor area??? If so, theres a fix that involves removing the cowl and replacing some plugs. Check out
Generation 2 Integra Club™ Forum there is a ton of information regarding these cars there.