The ferry system here provides a terrific service for commuters, campers and people headed to the Olympics and the coast. But I think the ferry can be a great under appreciated way for out of towners to appreciate and enjoy Seattle and the Puget Sound area.
If you are staying in Seattle, the ferry to Bainbridge Island is a 30 minute each way trip that lets you get awesome views of the Seattle skyline and Elliot Bay. The town of Winslow (on Bainbridge Island) is a pretty, picturesque place to window shop and grab some lunch before heading back. All for a minimal amount.
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