I have a 99 4 door accord with no sunroof, the windshield was replaced last year and for the pass four or five month when it rain water leaks in the on the passenger side(am in Germany so it rains all the time) i don't know where to start to fix this issue

 

It may be easiest to get a spray can of ruberized undercoating and begin to apply it to the underside of the car in select locations like the wheel well to sub-frame transition where water will spray hardest first. Then you could open the door and spray some in the hinge area and wire loom feedthrough, you can paint over it later if you like. Alot of water will run down this area. The other places are harder to get to, under the wiper cowl in the fresh air intake and you actually may have a clogged return to the door hinge are that is allowing water to puddle higher and overflow into the fresh air intake system.