I think it would probably work. I don't know a lot about alpacas, but what little I do know, has me believing that they do all of their pooping in just a few places, and not all over the pasture, like cows and horses. I would expect that if you have the animals and a farm of any size, that you have a loader of some kind -- front-end loader on a tractor, skid-steer with bucket, etc. If that is the case, you could certainly move the alpaca manure from their pooping centers, once or twice a week, to compost piles outside of the main watershed.

I'm not so concerned about the alpacas contaminating the pond, but that their urine and manure will add a heavy nutrient load to your pond that will result in uncontrollable algae and plants. A settling pond, or two, with lots of vegetative matter for the water to flow through on the way into the settling pond, and with water plants in the settling pond, can alleviate a lot of issues.

It sounds like you are dealing with an experienced excavating contractor. Talk to your local aquaculture extension service person also.

Regards,
Ken

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