Filters are designed to have water flow through them, and remove particles from the water. The filters becoming stained, or discolored, has little bearing on their ability to filter the water effectively. How well water flows through them is what's important. When you take something thats pure white, and expose it to dirt, filth and grime, IT'S GOING TO GET STAINED. So what? It still filters just fine. In fact, most filter manufacturers will tell you a filter will work better when slightly dirty. You could soak the filter in bleach to bleach out the staining. BUT, the bleach will also break down the fabric the filter is made of, reducing it's life. But then, at least it will "look" clean and you might feel better.