Lynyrd,
I am by no means an expert, in fact, I have made most of the mistakes possible, so your milage WILL vary.
I left a lot of "stuff" in the upper third on our big pond when we built it for just that reason, Habitat.
Here is what some of it looks like three years later.
One other thing to think about is all the nutrients the decaying matter will introduce to your pond as they decompose. If you need those nutrients like I did, you may not have a problem, but if your water is rich with nutrients, you may. As always around here, it depends.
For me, I am glad I left the brush and trees in the upper areas and I am also still happy I left some smaller trees on the east side for when the water rose. The habitat has bee used by the fish and birds. I now have active wood ducks and wood peckers in our trees. I see the Kingfishers and the occasional Eagle. I love it. The one thing to remember is that the nutrients WILL be used.
Here is a picture of the algae from this year, it is the reason I am going to try to grow Tilapia over winter. I am going to try to and produce several hundred pounds this winter and see if I can lessen the algae problem next year. On the other hand, I have seen a great deal of smaller fish in the algae this season, and the LMB are still doing great.
In moderation, everything (almost everything) is better.
