The present disclosure concerns an apparatus and system comprising closed bioreactors for aquaculture and harvesting. In certain embodiments, the system may comprise bags with various layers, including a thermal barrier layer, that may be used to contain the aquaculture and/or to thermally regulate the temperature of the aquaculture. The system may comprise various mechanisms for moving fluid within the system, such as a roller type mechanism, and may provide temperature regulation by compartmentalization of the fluid to regulate absorption of solar radiation and/or conductive or emissive heat loss and gain. Various mechanisms may be used to harvest aquatic organisms grown in the apparatus and process them into commercially useful products, such as biodiesel, methane, animal or human food, substrates for polymer synthesis or other chemical products.