A car gives you the most freedom on the main island. The paved highway runs from Ancud in the north through Castro to Quellón in the south; most of the UNESCO churches and outlying sights require turning off onto gravel roads. Car rental is available in Castro and Ancud. Fuel is more expensive than on the mainland, so fill up when you can.
Buses connect the main towns and run several times daily between Ancud, Castro, Chonchi, and Quellón. Local buses reach some of the smaller villages but services are infrequent — check times carefully or you'll find yourself waiting several hours for the return bus.
For the smaller islands in the archipelago — Quemchi, Dalcahue, Lemuy, Quinchao — small ferries run from ports on the eastern coast of the main island. The crossings are short and inexpensive. Dalcahue has particularly good ferry connections and its own excellent Sunday market.