Rottnest and the Swan River, where the crossing is the start of the day out.
Three of the Western Australian routes on this site go to Rottnest Island, Wadjemup, and all of them finish at the same place: the Main Jetty at Thomson Bay. SeaLink and Rottnest Express sail from Barrack Street Jetty in the city once a day each, and far more often from B Shed on Victoria Quay in Fremantle, where the terminal is being rebuilt around its passengers; from Hillarys Boat Harbour, north of the city, Rottnest Fast Ferries is the only operator and the car park is free. Every ticket to the island carries the Rottnest Island Authority's admission charge, collected by the operator when you book.
Choosing between the three ports is mostly a trade of time for convenience. The city boat follows the Swan down past Fremantle before it reaches open water; the Fremantle crossing is a short run straight out to the island. The other two routes stay on the river. Captain Cook Cruises' sightseeing boat to Fremantle follows the Swan down to Victoria Quay and sells that trip one way; Transperth's ferry from Elizabeth Quay Jetty to Mends Street in South Perth is ordinary public transport, paid with a SmartRider or a bank card, and free on Sundays for passengers who tag on and off.