The Roman mill complex of Barbegal in France is the largest preindustrial structure in Europe. Carbonate incrustations that formed from water flowing through basins, over flumes and waterwheels of the mill complex are partly preserved. The largest carbonate fragments are derived from three wooden flumes that once served the wheels of three mills in a train of eight. The deposits formed from the same water as it moved down from mill to mill. The shape, microstratigraphy and stable isotope patterns of the deposits of each flume reveal a unique history of use for each mill during the last 8 years of operation until their final abandonment. The sidewall carbonate deposits of the flumes vary in shape due to differences in the slope of the flumes during operation, associated with different‐size millwheels in different basins. At least one of the flumes must have been mobile and was uplifted to fit a millwheel of a different size. During 8 years, two millwheels were exchanged and one flume was taken out of action. Carbonate deposits from two flumes were subsequently reused for some unknown industrial purpose in a water basin, and one was later embedded as spolia in a building during late antiquity.