Tours leave from the Arco de Ponte Nova and head out into the Ria Formosa.
A couple of tours a day take a slower route through the Ria Formosa so you can take in the wildlife and a guide explains a bit about the area. Alternatively there are boats that go direct to the Ilha Deserta
On arrival at the Ilha Deserta you can have a quick look around and catch the boat straight back, or you can stay on the island and catch a later sailing.