There are several options for cruises within the Shoalwater Island Bay Park. You can take a 45 min cruise to Seal Island and Penguin Island. Hear the commentary on how the islands were 10,000 years ago, what the marine life is like. The cruise concludes on Penguin Island where you can spend as much time as you want before catching one of the hourly ferries back again. All cruises (except night cruises) include entry into the Discovery Centre on Penguin Island.
If you don't want to do a tour, you can simply take the ferry across to the Island and back again.
Penguin Island is around 50kms south of Perth and will take you around 40 mins to drive there. Take the Kiwinana Freeway to Thomas Rd Exit, through Rockingham Rd, Patterson Rd, Parkin St, Safety Bay Road to Shoalwater Road