Can you put your coop up on blocks? It would at least keep the water from going in when it rains. My feed and water for my chickens are in a covered area where water rarely reaches it. Water splashed onto the ground will keep it wet - mix anything organic in with that and you have a fly problem. Flies lay eggs and then you get maggots. You might also try some fly predators. They reproduce by killing the maggots and laying their eggs in the dead larvae. The more predators you have the less flies reproduce. The problem is that you have to sprinkle them out of range of your chickens as they think the larvae are a treat! However, the young predators can fly up to 150 feet to find maggots as hosts, so you don't have to put them directly in the coop. You can study about them online.
Your best bet is to keep the feed dry in the first place.