An aquaculture system which has a pen, a control system, a water pumping mechanism coupled to the pen, and a set of buoyancy tanks coupled to the pen. The pen can be disposed in a body of water and at least temporarily stores aquatic animals during development. The control system receives electric power from a power source and provides electric power to the water pumping mechanism to provides a flow of water through the pen. A portion of the control system is in fluid communication with the set of buoyancy tanks and adjusts a volume of fluid in at least one buoyancy tank to move the pen from a first position in which the pen is partially submerged in the body of water to a second position in which the pen is fully submerged in the body of water.