There are a lot of great places to run near water around the Seattle area but here are my top three:
For great people watching while running around a very pretty lake setting you just can't beat one or two trips around Greenlake...pretty much any time of day. The lake is encircled by a park so the views are generally trees and grass with a glimpse of the Space Needle and Seattle on the horizon—stunning around sunset.
Lake Washington Blvd./Seward Park
Another great running route...much less populated than Greenlake but every bit as pretty. During the summer there's boating activity all over, from cruisers to rowing club workouts. The sidewalk/running path is wide and uncrowded. And views are excellent.
Myrtle Edwards Park.
Starting at Pier 70 and running north toward Magnolia, this is a runners mecca. A lot of the people who trot here come from downtown Seattle, running along the waterfront piers then through the park. Astounding Puget Sound views include Alki Point, Bainbridge Island, Ferryboats, Freighters, Sailboats and incredible sunsets over the Olympics.