Methods and systems, including computer programs encoded on computer-storage media, for controlling a system for growing seaweed are described. Some implementations of a method include forming a substrate loop inoculated with seaweed spores; arranging the substrate loop about a pulley; submerging the substrate loop to grow the seaweed; determining, using a seaweed farm controller, that the seaweed has grown to a pre-determined size; and based on the determination that the seaweed has grown to a pre-determined size: providing instructions to the pulley to feed a section of the substrate loop to a harvesting unit; providing instructions to the harvesting unit to separate the seaweed attached to the section of the substrate loop; providing instructions to a cleaning unit to clean the section of the substrate loop that is freed from seaweed; and providing instructions to a seeding unit to inoculate the cleaned section of substrate loop with seaweed spores.