Exhibits in the main building include four permanent displays: Sandy Shores, Rocky Shores, Coastal Waters, and a changing exhibit area. The first features fish and invertebrates that live either close to shore or in bays such as Yaquina Bay. Progressing, the aquarium displays feature animals further offshore ending in a kelp forest and sea jelly exhibit. Flanking the permanent displays are the changing exhibits.

The largest exhibit is Passages of the Deep, in Keikos former tank, it features walk-through acrylic tubes surrounded by deep water marine animals such as sharks, rays, and rockfish.

The aviary at Oregon Coast Aquarium exhibits sea and shore birds. Those on display include the seabirds tufted puffin, common murre, rhinoceros auklet, pigeon guillemot, and the shore bird black oystercatcher. The seabird aviary includes two large pools and rocky cliffs.

The Aquarium has the largest outdoor Seabird Aviary in North America, which is home to tufted and horned puffins, black oystercatchers, common murres, rhinoceros auklets and pigeon guillemots. The Aquarium also exhibits two turkey vultures in a separate outdoor area. Outdoor exhibits also showcase marine mammal species native to the Oregon Coast, including sea otters, harbor seals and California sea lions. are the outdoor mammal exhibits. They contain sea otters, harbor seals, and sea lions. There is even a coastal cave that houses a giant Pacific octopus. The rocks in the outdoor exhibit are artificial rocks constructed of gunite. The Aquarium is also home to a nature trail that overlooks the Yaquina Bay estuary and features native plants and free-roaming wildlife.