Is this your filter?
[ame=http://www.amazon.com/Tetra-Whisper-In-Tank-Filter-3-Gallon/dp/B000HHQ712/ref=sr_1_1?ie=UTF8&qid=1344327974&sr=8-1&keywords=whisper+3i]Tetra Whisper In-Tank Filter 3I, 1 to 3-Gallon: Amazon.com: Pet Supplies[/ame]
The Tetra Whisper 3i is not an effective filter. The riser tube, which draws the water up, is so long that water only flows over the top portion of the filter. Take the cartridge out, look inside while it's running and you'll see what I mean.
You already have the air-pump. You can find a better sponge filter, cheap.