The Swinomish Channel is a peaceful body of water for paddling or rowing, though no local places rent boats. You’ll have to venture to Anacortes [1] for that; one of the more popular places there is Island Outfitters (2515 Commercial Ave.), which rents boats, paddles, and gear and runs guided excursions. Fishing and whale-watching charters also run out of Anacortes.
Those with their own boats can find short-term, first-come, first-serve moorage along the city-front Swinomish at floats located at the ends of Benton, Calhoun, and Washington Streets. Rates are $0.50 per foot per day, payable via self-serve drop box.
Links:
[1] http://www.moon.com/destinations/washington/san-juan-islands/anacortes