It silted up from alluvial deposits. You can find the same phenomenon happening elsewhere in the Mediterranean, like at Ephesus port, at Alexandria, or at Ostia/Portus at Rome. In some places, the Romans undertook dredging work to keep the ports open even in antiquity (Ephesus is a good example of this), but in the post-Roman period these areas quickly became unnavigable [is that a word? It is now.] In many cases, the topographical changes intensified in the post-Roman period as Roman earthworks, breakwaters/moles, and port installations became damaged and were not properly repaired to their original specifications (due to lack of water proof cement, for example). A good example of this is the disappearance of the Fayum, in Egypt, which was already "drying up" in the Roman Imperial Era but which was forcibly kept filled by Ptolemo-Roman water works connecting the Fayum to the Nile. In addition to silting, sea levels in the Mediterranean have changed since antiquity. I don't know very much about this topic, unfortunately, but my general understanding is that overall, sea levels in the Med have dropped risen [edit: I'm sea level dyslexic] since antiquity. This means what had been deeper bays would be more shallow anyway, even before factoring in alluvial deposition. Nevermind, I'm totally backwards about that. I'll just leave sea levels to the experts!

You can read more about Ephesus' port here. I was unable to find much information on the Guadalquivir/Baetis, but the situation is much the same. You can see an identical process happening at Cadiz. Check out this map of ancient Cadiz.