Understanding host, microbiome and environment interactions is key to optimizing an animals’ overall health and feed utilization. Unlike terrestrial animals, fish live in a three-dimensional milieu of microbes and therefore understanding these interactions is of upmost importance for aquaculture. In this project replicant samples were taken from three different rainbow trout production facilities which included environmental- (diets, water, raceway biofilms) and and host-associated (gill, skin mucosa, intestinal mucosa and digesta of fish). The facilities varied in configuration, and number of water uses (either 4 or 8 passes), but the set of samples obtained included triplicate raceway samples from each rearing unit. Using 16SrRNA gene sequencing, samples were characterized for relative microbiome richness and diversity (Fig 1). Within this large and complicated data set the goal is to determine the variance within water usage across replicate raceways within and between facilities and analyze for significant changes between water usages, across disparate sample types. Furthermore, our study highlights relative pathogen levels across sample-types and rearing units and will ultimately be used to evaluate interactions with on-farm water quality. An example of this is demonstrated in Figure 2 where the relative abundance of the bacterial pathogens Aeromonas and Flavobacterium are presented for the water and fish skin in 3rd-use water. Further in-depth analyses from this large-scale dataset will be presented. This is study serves as an initial study to determine on-farm microbiome compositions in production-scale systems and how they vary within and between farms. As nearly all aquaculture microbiome results presented in the literature being from laboratory studies, this is among the first microbiome studies conducted in production conditions, providing valuable insight for future studies.