Swanson Harbor, where Icy Strait, Lynn Canal, and Chatham Strait all meet up, is a popular anchorage. But a word of caution for boaters who are not local: stay clear of the reef, known as Sharp Ledge, on the southwest side of the entrance. Stay on a course for Rocky Island until well past the kelp. When leaving the harbor it can be tempting to turn west into Icy Strait towards Glacier Bay too soon. Also be aware of a drying spit at the NW tip of Couverden Island just outside the State float.
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I think I have mentioned this before that winters in SE Alaska are hard on boats. Most remain moored at a slip in a harbor such as Harris, Aurora or Auke Bay in the Juneau area or at marinas in communities such as Hoonah, Kake, Wrangell, Petersburg, or Ketchikan. You double your dock ties, drain your water systems and leave your boat connected to shore power with interior heaters. That is about all you can do except worry. Come spring you lift your boat out, pressure wash the bottom and change the zincs and de-winterize.