I think you're assuming that a normal Jedi would have to breathe as much as a normal human. We know, from Phantom Menace, that Jedi can hold their breath for an extended time. So, presumably, they can control their bodies to require less oxygen.
But the breather doesn't necessarily filter air from water. According to the Starwars.com Databank (emphasis mine)
A small breather that fits snugly into a Jedi Knight's utility belt, the A99 aquata breather is a compact mouthpiece designed to supply its wearer with a breathable gas. The A99 has advanced filters to allow it to function underwater, in a vacuum, and in certain poisonous environments. The A99 has a number of variants to accommodate a variety of alien physiologies. The A99's miniature compressed air tanks can supply two hours of oxygen.