Amtrak Cascades runs trains and buses between Seattle and Vancouver: http://www.wsdot.wa.gov/amtrak/

Ferrytravel.com povides all the details on travel in the Northwest: http://www.ferrytravel.com/

You may want to ferry from Seattle to Victoria, then ferry on to Vancouver, finally taking the train back to Seattle. Of course, I am assuming from your post that you are flying into Seattle :)

I hope you are planning to stay overnight in Victoria, it is a lovely city with lots to do. If you go to Butchart Gardens, there are buses that leave throughout the day from the main pus terminal. Be sure to catch the very first one, as it arrives at Butchart long before the tour buses start getting there. Very few people are at the gardens that early, allowing you to explore and then return to Victoria before the crowds take over.

If you are traveling lite, the Seattle ferry terminal is a pleasant walk from many of the downtown hotels.

Michele, Oakland, CA