Hmmm...more input, please.
How did you manage to cut the holes? I mean, I assume that you bored the holes with some sort of augur...right? How far below the level of the ground water do you have to go to hit firm, undisturbed soil? Is the soil so firm that the hole is not collapsing?...this would be a blessing.
I personally don't know the professional answer, but I do know that the best concrete pour is a continuous pour. I guess my first reaction is if you are able to bore to a firm soil footing, the hole doesn't collapse, and you have a foot or two of water within this hole, I'm thinking that the best approach would be to have a pump on hand to suck out as much water as possible moments before you dump in the concrete...one pier at a time. The concrete mix will displace any remaining water in the bottom, but it would be adviseable to have enough prepared to get above the water level in one shot (ie; a concrete truck). If you use a truck, they can control the mix to keep it on the dry side. I would also consider some small rebar cages.
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All that being said, I am not an expert on this one. I would be doing the same thing; asking. I have very good contacts at my end with the concrete industry. If none of the PB'ers has true, practical experience to get your answer, I can get it later on this week.