We used two sediment cores from the ancient harbour of Rome (Italy) for palaeoenvironmental reconstruction. The imperial harbour of Rome and its town, Portus, were constructed in the Tiber Delta area. Today, they are similar to 3 km from the coast, close to Leonardo da Vinci International Airport. The port was excavated during the reign of Emperor Claudius, inaugurated by Nero in 64 AD, and substantially enlarged under Emperor Trajan. This paper focuses on analyses of ostracods in sediment cores from the harbour and provides insights into the palaeoenvironmental evolution of the harbour water bodies. Pollen data complement this ostracod-based reconstruction, providing information about the vegetation around the port. One core (PTS13) was taken from the dock area (darsena) excavated at the time of Claudius. The second core (PTS5) was collected from the Trasverso Channel (Canale Trasverso), excavated after the port inauguration and later dredged during the fourth century AD because it had filled in with silt. Radiocarbon, archaeological and pollen data indicate the two cores overlap in time slightly, or perhaps not at all, the core from the dock site (PTS13) containing the older record. Ostracods recovered from the two sites represent very different aquatic environments, driven in one case by the Tiber River input and in the other by "marine" harbour waters. Parallel study of ostracods and pollen in the cores reveals the impact of harbour management activities, which are linked to ship hull maintenance, as well as erosion and siltation in this coastal setting.