The data from this project was used to determine what bacteria are prevalent in different Atlantic salmon RAS hatchery systems in Tasmania and which taxa successively transfer at each life or operational stage. For the experiments data was mostly tracked in two hatcheries and examined microbiota from eggs, alevin, fry, parr, smolt, during smoltification and farm transfer, and the first few months of farm feeding ending with post-smolt. Sampling included surface swabbing of fish (parr and smolt), intestinal/digesta samples. This dataset comprises smolt and post-smolt associated bacteria assessed by 16S rRNA gene amplicon (V1-V3 region) 300 bp pair end sequencing. The smolt were reared in the Rookwood hatchery located in Tasmania and transferred to farms in the D'Entrecasteux Channel. The extensive dataset complements multi-year sampling of Atlantic salmon in sea cages as well as other metadata collected from the hatcheries and farms, including microbiota data for feed and water.