Washington State operates the ferry service as part of the Washington State Department of Transportation. It has ten routes servicing twenty terminals and serves roughly 24 million passengers in 2016. There are currently 22 ferries on the Puget Sound. The largest of the ferries carries 2500 passengers and over 200 vehicles.
Rates on the ferry fluctuate during the summer months as the tourist traffic increases and the rates go up accordingly. You can find information on these rate schedules HERE .
Trips to Whidbey Island can get very busy in the summer time. You will take the Mukilteo ferry over to Clinton with schedules almost every half and hour, but be prepared to come early and get in the ferry lines, they tend to have a 90 minute wait. The Coupeville ferry from Port Townsend to Whidbey Island in Coupeville requires reservations, and they fill up quickly, so plan accordingly.