What is causing the smell is that it is wet. The waterer may be leaking or spilling water. You may be getting water in from outside somehow, either through the roof, vents, doors, windows, walls, or it is seeping up from underneath if it is in a low spot where water drains to. But what it sounds like is that the chickens are in a fairly small coop and the poop is just building up too thick to dry. Maybe a combination of these.
So what can you do about it? First, determine the cause. Then address the cause. Until you know the cause of the moisture, you can’t fix it.
Some things that might help though it’s hard to know what to suggest when you don’t know the real cause.
Build a secure run so they can get outside. Reduce the poop load in the coop. A droppings board can really help with that too. A lot! Make sure you have plenty of ventilation so the poop and bedding can dry out. Regularly stir the bedding so it dried out better or occasionally toss some corn on the bedding so the chickens will scratch it around for you.
I clean the bedding out of my coop about once every four years. I scrape my droppings board about once every two weeks. But I have a large walk-in coop with a limited number of chickens so it is not overcrowded. I keep it dry. Mine spend a lot of time outside, not in the coop. Occasionally some rain or snow will blow in, but with a lot of ventilation and buy encouraging them stirring the floor with scratching, it dries out pretty fast. Mine is pine shavings over dirt. It’s on a bit of a rise so rainwater does not run into it from below.
I don’t know what your coop looks like or how crowded it is, but you obviously don’t have a situation like mine. You’ll have to work a lot harder than I do to maintain yours, but giving them more room if you can ill help. Good luck!