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Abstract The frequency of skeletal deformations in fish is a common biomarker when investigating the environmental response to effluents of various origins. This study discovered a new biomarker: elevated mineralization levels of the vertebrae in the caudal region of perch Perca fluviatilis. The study was conducted in northern Sweden in lakes receiving discharges from an iron ore mine and adjacent reference lakes. The field observation was followed up with an egg‐hatching experiment showing a similar lake‐specific pattern in hatching and deformation frequencies in larvae.