As the global population continues to increase, so to does the need for a sufficient and sustainable source of protein for human consumption. In line with this need, aquaculture production of finfish including Atlantic salmon (Salmo salar) is undergoing an expansion into land-based recirculating aquaculture systems (RAS). Little is known about the impact of the tightly controlled RAS environment on an important component of the immune system, the microbiome. Here we analyse the temporal dynamics of the skin and gill mucus associated microbiome of Atlantic salmon across smolt production in a RAS and in the first weeks post-seawater-transfer. Water and diet samples were also analysed.