I had a similar issue. Here is how to fix the problem.
1. Clean the filter media in your canister, everything EXCEPT the beneficial bacteria growing media (bio glass/coarse sponge/bio beeds).
2. Purchase carbon or purigen (if you use purigen only use seachem prime water conditioner or else your tank will make your room smell like chemicals because you used a different companys water conditioner, trust me.)
3. You have to understand that if all your filter media is clear, it takes 4-6 weeks on average for the nitrogen cycle to start up. In English, this means that there is no "good" bacteria growing in your filter on the filter media that aids in removing bad stuff from your tank. This process is often called "new tank syndrome" and when I didn't know anything about this, I was going crazy thinking my 150gallon filter couldn't keep a 55 gallon tank clean for more than 1 week.
4. What keeps water clean is usually white floss pads and carbon, so make sure you clean and rinse the floss pads and buy/replace your carbon every 2 weeks.
