There is a program named Lake Management Solution (developed by Commerce Systems Group) it uses Microsoft Dynamics NAV software. As far as I can tell however it seems to be aimed more at resource planning than actual lake management.
I found another software, ironically enough named Aquanate, that seems to be geared toward fish farm production.
If you search on agricultural management software there are many vendors that sell software geared toward managing farms. Perhaps something along those lines could work.
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As an also and besides I have been researching farm taxation and accounting lately. I have been amazed by the level of technology utilized by many of today's farmers. GPS technology combined with software to track, crop yield, fertilizer efficiency, etc, etc.