| Summary: | The objective of this study was to report the prevalence of deformed Atlantic salmon (Salmo salar) embryos across a range of incubation habitats. We assessed 3234 embryos that had been incubated to approximately the “eyed” stage in simulated redds at 20 sites in 7 rivers across 2 basins (the Tobique and the Miramichi River basins of northern New Brunswick, Canada) over 3 winters (2012-2015). A range of incubation habitats were represented: regulated rivers warmed by bottom-draw dams; unregulated, ice-covered rivers of different sizes; and a long-residence groundwater-fed brook that remained ice-free. Deformities were unusually prevalent (1.4-95.7% deformed) in the Tobique River basin compared with the Miramichi River basin and hatchery controls (1.1%). Within the Tobique River basin, warmer sites near dams had the fewest deformities. This dataset includes the deformity prevalences (deformed/normal, and deformity type) for each sample in this study.
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