It doesn't effect it that much. Putting it in the top bucket only aerates the water when the top bucket is filled, only accomplishing half of the two-fold goal: provide oxygen to the roots, and to inhibit algae growth. These little impeller pumps aren't severely effected by bubbles in the water, and I've had this bucket running for months now without any problems.

Thanks! There's a few benefits to supplying air to the roots. First, it kills off pathogens that live in the water but cannot live in air, which keeps the nutrient solution fresher longer. Secondly, adding air into the nutrient solution changes the electrical charge of the solution making it easier for the roots to break down and assimilate the nutrients. Roots will use as much oxygen as they can get, so while keeping the nutrient solution aerated is nice, it helps to feed the roots in a flood/drain system like thism since while flooded, the roots are still getting oxygen. One other advantage of the flood/drain system is that root rot is a dramatically lower risk. The best advantage that any hydroponics system has over a soil-based system is that you have ultimate control over the nutrients that the plants get. This means that you're able to adjust your nutrients to fit particular plants and promote optimal growth, which in turn grows healthier, faster, and produces bigger and higher quality fruits. You just don't have this same level of control over a soil-based system.

Check out the pic on the last page. I don't have access to the original finished bucket that's growing plants, just this one that I built for this instructable. Enjoy!