Brettski,
I am guessing that your property will get managed just like your pond, with you taking care of its needs.
I know you have set your goals, so what you are dealing with now are the choices as a result of the goals. Probably no different than your everyday routine, only a different scale.
Dealing with the muskrats is your answer to your question, yep you are going to manage the environment on your property.
I think all of us do to some extent or other. My new pond has less than a dozen fish remaining from 1100 that were stocked as a result of me not doing anything. The heron and little cormorants had a different set of goals than me.