Kasey, I just went through the same thing with my pond. I had some shallow weedy areas I wanted to get rid of and expand the size. I rented a rather large excavator with wide tracks, two yard bucket. It did a great job of digging the muck and peat/cattail roots out of the pond. Most of my pond has steep edges which has worked great to control weeds. I too was very afraid that the low water level that turned to chocolate milk would kill the fish. They made it through fine. Nice to hear from another MN pond owner. I'm afraid that if you have high nutrient levels caused by past elk herd and by your fish you will have a duck weed problem. I'm afraid to use chemicals to kill DW in muy pond because we eat the fish. I don't care what anyone says it can't be good to eat from water with herbicides in it. Looks to me like your pond would be the perfect place to use the Pond Boss prickly rope. Some posts on that approach can be found somewhere amongst the "controlling unwanted plants" topic I think. You should give it a try next year.