Possibly the best way to get a feel for San Diego is to see it from the water, and San Diego Harbor Excursions is more than happy to oblige.
You can take a one- or two-hour narrated tour of the harbor and get a good look at the US Navy fleet, the shipyard, and the San Diego skyline. The one-hour cruise covers 12 miles every day, year round; the two-hour cruise twice that. You can also hop the ferry to The Ferry Landing Place in Coronado, a tourist center that has shops, restaurants, and the chance to rent bicycles for a land tour.
The tours don't provide much depth, and children may find the two hours way too long, but it's a reasonably nice introduction to this old port town.
The ferries shuttle between the Broadway Pier and Coronado every hour from 9am (The Pier) or 9:30am (Coronado) to 9pm (The Pier) to 9:30pm (Coronado). You can buy tickets at either place, or email for reservations.
Whale Watching: From mid-December through March you can take a 3 1/2 hour trip tracing the migration route of the California Gray Whale.
Water Taxi: Another service is the water taxi. Call for routes and schedules (619.235.8294).
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