There is bad smell coming from the vents when i turn the air or heater on, does anybody know what the problem might be? Water in the canals maybe ?

 

dead rat/mouse

 

Girlfriend's underwear?

 

Algae and **** is clogged up in the evaporator drain causing water to sit inside the box and start smelling bad. Stick a long pipe cleaner up into the drain tube that comes out from under the car (the one that drips water when you have your A/C on) and it should clear that sucker out. just stay out of the way when you clean it out because nasty green water will probably splash everywhere. afterwards spray some air freshener into the cowl in front of the windsheild and crank the A/C.

 

yea bro.... you might just have your headers craked.....you need to weld them and stop the air from coming out...your air vent are in front of your headers so if its coming through your vent make shure envrything is tight or check if your headers are cracked...

 

It's probably some mold, my brother's TC had the same problem he installed a cabin air filter(Doesn't come with one from factory) and it doesn't smell anymore.
Don't know if 98 Civics have cabin air filters though.

EDIT: If you want to test for a cracked header, put a little seafoam in the brake booster. Found a leak in my 89 Hatch that way.

 

Probably not a cracked header if it doesn't smell like exhaust. The smell is most likey something dead/decomposing (sp?) under the dash or in the engine bay, or the drain hose is clogged and water has back up into the evaporator and is no stagnant goo.