Chquinta,
I had the same problem. My chicken coop and run are on the back of my property which is unfortunately the lowest spot. I had terrible problems with flooding in the beginning. I am going on my second year with chickens and we have made several modifications from our original setup. The original setup was a 6 x 12 foot wire dog kennel with a modified old shed for a coop. The shed/coop was sitting on pallets and a tin roof was over the whole thing. Had a lot of problems with mice and other things wanting to live under the coop and the whole thing turned into a huge muddy mess every time it rained. The bottom of the dog kennel was rusting from sitting in the water and mud. We expanded the pen (I found a couple of more dog kennels for cheap or free on craigslist and freecycle) and I put bricks (free from freecycle) underneath of the bottom of the pen and then brought in dirt and filled it in. The inside of the pen is now higher than the ground around it and drains off pretty well so my chicks are not constantly in the mud. The tin roof keeps away the hawks and keeps things relatively dry. This past summer we built a new and bigger coop to replace the original and it is 3 ft above the ground. The chickens have a little ramp to get up into it and they are able to scratch around in the dirt underneath. The new pen/coop area is now about 20 x 30. The tin roof covers a 12 x 20 area the remainder just has a wire roof. Lots and lots of room for my 8 hens and 1 rooster. I plan on greatly expanding my flock this year, just having trouble deciding what kind of chickens I want.
Hope this helps you. Like everything in life, keeping chickens has been a learning experience for me. Good luck!!