Derek,
Your site description indicates that the job can be fairly predictable, provided you offer very specific dimensions and excavation requirements. (sorry to hear about the NRCS response....something sounds askew with their attitude?) Anyway, as Tuzz mentioned, there are some unknowns, but a skilled pond contractor will know the region and be versed in what they may possibly be. All this being said, the guy that I am currently working with will straight bid a job if he can easily see the scope of the work. Then, as a free/included option, he will track the hours of equipment time at a specific price per pc of equipment (currently at $100/hr). If at the end of the job the equipment time comes in under the quote, he will only bill the equipment time. He says that he is the exception to the rule in "the land of excavators", but his customer base appreciates it..and..he claims that most times he comes in under his bid. In my project, because I am working with a site that was 4 - 6 acres, heavy timber and thick bramble, and I brought him in late Spring 2005 (heavy leave-age) and I wanted to start in August, he was uncomfortable in a straight bid because it was too difficult to "see". He asked me if I would go with straight equipment time at $100/hr. I agreed, based on the super reputation he had in the area....then I spent many hours at the jobsite watching the performance to confirm my bang for the buck. He delivered. If I thought he was slacking, I would have politely asked him to provided the equipment time log, match it to mine, ask for a bill, and fire him.
My point: I think it might be fair to ask a contractor that is doing an "easy to see" job to provide a firm bid and offer a "by-the-hour" option. Then, watch him right from the beginning to verify it's gonna be a good performance....and....don't be afraid to pull the plug.

Afterthought: Ya know, there is one story that I would like to share with all the pond-sters that is pertinent. I mentioned in the above post that my bro' did a 3.5a pond in the U.P. forest bottom-lands. He went thru he-- to get there. His phase one was about 1.5a and it went fairly smooth (except for the week that he decided to rent a dozer and do it himself....that turned out to be a do-it-yourself catastrophy; he bailed out, lost a small bunch'o $, and hired in a pro to finish). Anyway, phase 2 is the kicker. He hires the local excavator (different from phase 1) and gets a commitment to do the job during the ideal window at the end of summer. According to my bro', the window in U.P. is v limited. Anyway, the window comes and goes because his contractor is busy with other (more important?) clients. Then, when the contractor is ready, the window is gone and things are gettin' wet.....he shows up with the equipment and tears into it. The next $30,000 + of time was spent slipping and sliding; the contractor blaming nature for the $ overage. He hands my bro' the bill and the war begins. Ultimately, they avoided court by negotiating to low $20k's and their friendship is ruined (awww, too bad, ya-hey). The Moral (as if I need to tell ya): even at a higher price, get a guy that is honest and you can trust.