A pneumatically controlled shellfish aquaculture apparatus and method for growing shellfish using the apparatus are provided. A frame has containers for holding shellfish secured to the top side of the frame and tanks secured to the bottom side of the frame. Each tank has an air supply line connected to the tank and an opening on the bottom side of the tank. Each air supply line is connected to a manifold for controlling airflow to the tanks. Air is used to displace water in the tanks by pushing the water out of the openings in the bottom of the tanks in order to float the frame. To submerge the frame, the tanks are depressurized to allow water to displace the air in the tanks. When floating, the tanks lift the frame and the containers out of the water to allow air desiccation in order to prevent bio-fouling of the equipment and shellfish.