Apologies, I assumed you were currently cycling a tank.
Most of the bacteria that processes ammonia and nitrite will live in the filter media, I don't think you will find very much in the water. There might be some on gravel, particularly if you have an under gravel filter (although these don't seem to be very common).
Last week I emptied the water and gravel from a tank and replaced all the water without any gravel and the tank is still processing ammonia as before.
So when cycling a new tank, try and and add mature filter media from the beginning, this should speed up the cycle quite a bit. Keep in mind that the media should be always be kept wet and should be moved as quickly as possible.
Hope that helps!