i doubt it, youd be circulating air, but if youre really worried about things getting stale take a clear air hose and put it at the bottom of the bowl, which will be the top when its in the tank, and run the other end under the rim of the bowl, across the bottom of ur main tank, up the side and out the top of the main tank. this will keep new air circulating in and out of the system and should keep your water from getting stale. you could even do 2 of those air hoses leaving the end of one in the water of the fish bowl that way you could do water changes if you felt the needed... siphon the water out, then use a funnel to add some water or something through the second hose while air is still able to go in and out of the first hose. essentially a tank inside a tank. youll have your fountain and can still treat your bowl with meds for algae if need be.