Well, we've already ordered the windmill, so we're committed there. We don't want the electricity costs, and the labor of burying the line, and it seems that our pond is way undersized for the windmill's capacities. The house is 400 feet from the pond. I had read how that can be done (compressor near house for electricity and then air line to pond), but the windmill seemed like a one-time, up front investment in maintenance-free and somewhat constant aeration. (We've read about people putting compressors on timers anyways, and here in the mountains of WV, we get a pretty steady breeze year round.) I hope it's the right choice! We'll see.
The aeration will provide some movement to the plants over top of the barrier; so will convection currents due to temperature changes (warm water flowing down as cold water sinks), and general water flow through the barrier, since we are planning to construct a non-standard barrier (more on this below). At least, that's the theory.
We have bats that eat mosquitoes and there will be frogs and salamanders and dragonflies. We have VERY few mosquitoes here and, remember, the whole pond has been stagnant for years (both ponds, actually) without increased mosquito populations, so we don't THINK that's an issue.
The fish, if present, wouldn't stay in the plant zone. It's fluid between them. The design includes a standard 2" of water flow allowance near the surface over the barrier, and we're planning on increasing the permeability from the standard liner/solid/stone/wood barriers that natural swimming ponds usually have. Instead: we're using recycled pallets and fence posts, and back-filling the regeneration zone (plants) with larger-than-gravel rocks from piles left on our farm by generations before us. This is a compromise: it's less surface area for the good bacteria to attach to, but larger rocks provide more gaps for the water to circulate. Good bacteria will also find homes on the exposed plant roots, we hope.
Anyways: keep those ideas coming. Thanks for the lime idea: where do you buy it? (BTW: because this is a spring-fed pond, everything flows down to our neighbor's farm, so we have to be VERY careful about what we put in our water.)
Pictures: Instead of giving away my photo rights, I'm posting a link to my photo record of the progress so far. First picture is our farm in 2012, when the pond was being dredged in the middle of winter. It's to the right of the larger of the two sheds in the foreground. House is on the far right; it's yellow.
The rest of the pictures are ordered sequentially; the siphon draining began on 9/2 in the evening, and we started to construct the barrier using pallets and fence posts on 9/6. Water is shown as of today (9/7) with about 1-2 more days of drainage left, assuming we don't lose our siphon.
(More pictures to be added as we go.)
Photo album of pond progress 
