Freshwater mussels are sensitive to contaminants, particularly in early life stages which has contributed to widespread population declines across North America. Historically, the Clinton River Watershed, had a thriving and diverse mussel population. In past decades, chronic anthropogenic disturbances and contaminants in the agricultural/urban watershed have reduced mussel populations. Recent remediation efforts have substantially increased water quality, and mussel augmentation efforts began in 2024 to re-introduce laboratory-reared Fatmucket (Lampsilis siliquoidea). Juvenile mussels were measured and deployed into flow-through mussel silos at five locations for three months to assess site suitability across the watershed. Sondes were deployed to continuously measure dissolved oxygen, water temperature, conductivity, and depth. At the end of the deployment period, juvenile mussels were measured, and their digestive glands were dissected for microbiome and transcriptome analysis. DNA and RNA were co-extracted and sequenced. Sonde measurements were used to estimate stream metabolism over the mussel deployment period. We found that all the sites were suitable for mussel re-introduction as we observed minimal juvenile mussel mortality in the silos and adequate water quality during the deployment period. We found some evidence that mussel growth was correlated with stream metabolism, where the fastest mussel growth rates were measured at the sites with the highest estimated gross primary productivity. Within the mussel microbiome, we determined that longitudinal connectivity was an important factor in shaping the microbiome community, but that all sites except the two closest sites (<1 mile) had distinct microbiome communities. Interestingly, we found overall microbiome function was similar among all assessed sites. We are currently analyzing the mussel transcriptomes to gain further insight into juvenile mussel gene expression at each site during deployment in the silos. This work provides insight into mussel health, including stressors, during deployment and demonstrates endpoints to consider during site assessment for augmentation.