Just three of them jump to mind, but there must be many more examples where changing geography left cities built on sea-going commerce sitting on silted rivers, and further from the ocean.
I am thinking of Florence, Seville, and Pisa. Oh - Pompeii was a seaport too, which is partly why it was so full of whorehouses. Whorehouses and temples and fast food joints - that was Pompeii. Here's The lost harbour of Pisa revealed
Classic visit to Pisa (which is actually a charming antique town like San Gimignano or Siena): Grab a slice of pizza, take a selfie in front of the bell tower, then get back on the air-conditioned bus.
Other examples of cities which were once important seaports?