Any filter media that catches "stuff" is not helping with your nitrate problem. If you leave the "stuff" in the water, it will continue to break down, and will do so quickly in high flow areas). This organic matter becomes ammonia->nitrite->nitrate. The best solution is to remove as much as possible before it breaks down. This is best accomplished through skimming. If you choose to run any mechanical filter media (filter floss, sponge, bag, etc.) you should clean it daily to remove the "stuff" that is collected.