I have a scenic megan alize 1999 with two sunroofs. I had water coming into the two front foot wells, water into the rear foot well compartments and water into the spare tyre compartment. I have followed the advice of removing the plastic wheel arches as much as I could, and did in fact find the drains pipes as others have said. They were clear plastic with black rubber bungs on the end, all in inches of mud. The pipes are lower down that I expected and came out of the bulk head from the direction of the drivers side. As soon as I removed the bungs (which just slid off the pipes) a lot of water came out. I then removed all the mud by hand. I now await for it to rain again to see if this has solved the problem, but the logic seems right. Note, that I only needed to removed the one screw (top most) which holds the inner plastic wheel arch in place. I then got a screw driver and put it under the plastic cover approaching from the other end of the plastic and scooped it around the wheel arch lifting the plastic cover off up to the screw I never took off. The drainage pipe was immediately visible and the problem obvious. Good luck everyone - it can be sorted!
Peter Hodgetts, November 2013