It's pretty cool how the hexagonal harbour has survived. It's a lake now, Lago Traiano, about 2km inland.
Here's a poster with some progress drawings over the millennia: https://www.academia.edu/29407769/The_effect_of_the_Tiber_de...
So, the Tiber deposited silt in front of the port. Reading https://en.wikipedia.org/wiki/Portus, that isn’t surprising. It says:
”Claudius constructed the first harbour on the Portus site, 4 km (2.5 mi) north of Ostia, enclosing an area of 69 hectares (170 acres), with two long curving moles projecting into the sea, and an artificial island, bearing a lighthouse, in the centre of the space between them.”
Those constructs must have decreased water flow, allowing (more) silt to settle.