In vertebrate morphology, the notochord is seen as changing from a dominant axial system in embryos to a remnant in most adults. That view underplays the functional role of the notochord throughout development and in different body regions. Its dynamic functional morphology is highlighted by the complex life cycle of the Atlantic salmon, Salmo salar. Embryos hatch as alevins that burrow into gravel of the riverbed. Alevins emerge as fry to explore the bottom. Parr patrol the water column as active predators, and smolt migrate from river to sea, returning as adults to spawn. Does the life cycle of the whole animal match that of the notochord? To address this question we used a variety of techniques to track structural changes over time and across body regions. The notochord in the middle of the body is dominated by chordocytes that form vacuoles in fry, exchange vacuoles for extracellular lacunae in parr, regain them as smolts, and retain them as adults. The vacuoles and lacunae are correlated with changes in the hydrostatic pressure of the notochord that underscore how stiffness enhances locomotion. The situation is different for the notochord in the cranium and the caudal fin. The cranial portion forms an unsegmented bony cap that is then degraded by osteoclasts. The notochord in the caudal fin never forms bone in its sheath; instead, partial and robust transverse septae form from the sheath and are retained in adults. That the notochord changes continually and varies dramatically in different body regions highlights the dynamism of this fundamental vertebrate organ.