That's most likely the reason. You should have a filter and a bio-filter. You never change them both at the same time. The bio-filter harbors bacteria which neutralizes the fish urine. Yes, it will not seem 'clean' but it doesn't matter. Anyway, you should change out the water a bit at a time. Imagine that the water is water in a glass. If you let it evaporate halfway, and add more water, then eventually that water will get cloudy as the concentration of minerals increases. Minerals don't evaporate, so that water gets more and more concentrated minerals. You have to remove about 10% of the water a week and replace it, to keep the water normal. You could also use distilled water, which I've had success in starting a new tank, but if you do clean out a tank, don't clean the bio filter and you need to let the new water sit for about 24 hours to let the chlorine dissipate.
>Change in chlorine?
Uh, there shouldn't be any chlorine in a fish tank. You and your roommate should probably look up fish care in google or something. The first link is to ASPCA and they do have good advice. I had an aquarium for several years, and if you don't know what you are doing, mollies or perhaps a plecostomus is a good choice. The pleco can survive pretty nasty water. However, they can grow pretty large and they would need a huge tank. They live about 10 years or more, so it's a big commitment. On the plus side, they will clean the sides of the tank.