An aquaculture system can include stacked growth trays. Animals, such as shrimp, can be transferred between the growth trays for different stages of growth. Waste water can be removed from the growth trays and can be processed by a water treatment system. Treated water can be returned to the growth trays. A valve in a first configuration can permit water to circulate through the growth tray, while impeding the animals from exiting the growth tray. In a second configuration, the valve can permit the animals to exit the growth tray, such as for transition to a subsequent growth tray. A sweeper system can be used for cleaning and/or mixing the water in the growth tray, and/or for pushing the animals out of the growth tray during a transition.
