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Ancient harbours are rich archives of human-environment interaction. However, dating harbour deposits and correlating their stratigraphy is a major challenge because of typically high sedimentation rates over short periods and possible curative dredging events. Portus, the maritime harbour of Rome at the height of the Roman Empire, was a port complex composed of basins and canals connecting the commercial harbour to Rome via the Tiber River. Sediment core CPS1 in the narrowest of these canals, Canale Traverso, is located centrally in what was the capital city's commercial hub and contains a continuous harbour depositional record with average sedimentation rates greater than 1 cm per year. Here we use piston coring, high-resolution core scanning and a multi-proxy sediment analysis including for the first time paleo- and rock-magnetism, and bulk and clay mineralogy in order to overcome the problems of dating harbour deposits and correlating their stratigraphy. The method allowed precise identification of major reworked events, including a dredged deposit and a hyperpycnal deposit, which improve the chronostratigraphy and water depth reconstruction, and sheds light on harbour technologies at the height of the Roman Empire. A debris layer with abundant ceramic fragments and rocks marks the decommissioning of Canale Traverso and provides a new chronostratigraphic marker at Portus. Multi-proxy riverine input signatures point to the possible use of canal gate technology for water flow management.