Noviodunum was the headquarters of the Roman Imperial fleet Classis Flavia Moesica from the 1st c. AD. Its importance as a river port is shown by its description in various ancient sources and itineraria. The settlement is located on a limestone promontory on the right bank of the River Danube (Romania). Its location is highly strategic, as it is the last narrow crossing of the river before entering the Danube Delta and thereafter the Black Sea. Despite its advantageous position, the settlement location was geomorphologically challenging; issues of flooding, rising groundwater tables, drainage problems, mobility and erosion of the concave banks and sedimentary budget have all played a role in the evolution of the site, and in turn, the location and preservation of archaeological remains. Understanding the processes operating in this dynamic environment has required an interdisciplinary research study. Here we present the results of a multi-proxy approach combining bio-sedimentology, granulometry, statistical analysis and archaeology. Our geoarchaeological research aimed to (1) understand the Danube’s palaeodynamics in order to (2) locate and characterise the harbours.Our findings suggest the existence of two possible harbour basins, upstream and downstream of the fortress, that functioned until at least the 5th c. AD.