We are only 2 miles from a major river and I see bald eagles all the time. I've even had one perch on a tree on our land. They're beautiful. I have covered runs and have never encountered an issue with them. As long as the river isn't frozen over, they spend most of their dinner time there. I enjoy having them around. I will say that someone a few miles away does not have a covered run, and he did get to untangle an eagle from his pen one year when everything was frozen. (It seemed ok when it flew away.) I wouldn't be terribly worried if your birds have cover.
We never had baldies even look at my fowl. The are either fish or carrion eaters, rarely anything else so enjoy the view. When we have butcher days we get about 3-4 of them together with golden eagles and vultures gathering at the gut/refuse pile. Its cool to watch.
We did have a golden eagle pick up and carry off one of our cats. Our 20 lb black and white tom cat was sunbathing on the horse pasture and whoosh came down the eagle grabbed him and was gone...... bye bye kitty....... Never liked that cat so I honestly don't miss him.
Cover your run with netting and only allow closely supervised free-range time.
Pretty bird. Funny story- a few years back my daughter (2 y.o. at the time) was playing in her sandbox, so she was crouched over, puttering in the sand. A Golden Eagle spotted her and apparently thought she was edible. It did this huge swoop downward and dropped out of the sky like a stone toward her. She sat up suddenly, still completely unaware that anything was going on. That eagle practically twisted itself inside out trying to put on the brakes, missed her by about 10 feet, landed awkwardly in a nearby tree and almost fell off the branch, before finally taking off. I didn't even have time to scream. That was the first, last and only time I have seen a Golden around here. Scared the life out of me. My daughter never even realized anything had happened.
I have bald eagles in my trees all the time. Ive never had one bother my chickens. Now if I throw a dead coon in the back of the pasture, they come running. They seem to prefer dead animals over live. Just enjoy them!
I live about a mile off a large river in Michigan and bald eagles love to roost up in a dead tree in my backyard. I would be more worried about hawks than bald eagles. I have never had a problem with eagles even checking out my uncovered run. Hawks on the other hand are smaller, faster, and a whole lot more determined to get themselves a fresh chicken lunch. I wouldn't stress myself out worring about it. If the flock feels threatened, they'll run for the coop.