A large city, by the sea, will be open to invasion.
So I suggest the following things for these sea-cities, as well as for some land-locked cities.
A system of fortifications along the waterline, or at least a system of long walls, intersecting each other, to prevent a direct approach from an landing or marine force. You could call it something as simple as the Longwalls as the Athenians did, or something like the Tesserae (the block, or the cube).
A cistern system. If the city were walled by land and fortified by sea to withstand a siege then it would need to assure a fresh water system. Ordinarily that would be the nearby river, but if invaded then the river could be diverted and the water cut off. You'd need an underground cistern system, in bedrock (maybe coated in marble, not a sandy foundation or of shale) that was at least partially filled at all times. Empty cisterns could be used for supply storage and even as secret escape passages or bunkers for VIPs. You could call such a cistern system something like, the Hularion, named after the architect who designed it. The Hularion would be an opens secret to the people of the city but not generally spoken of to foreigners.
A large city, which was thriving, would probably need a museum of some kind, probably attached to their library system. I am using the word museum not as it is used today, but as the Greeks used it. A museum was a place where one went to be inspired by the "Muses" and a vast number of things went on there, everything from repairing and inscribing scrolls and books, to the writing of plays, to the recording of history, to workshops for inventing new products and even to the invention of weapons or war and new types and methods of defense. You could call such a museum anything from the Luminaria to the Operatum. Or you could just call it the Museum.
The Refractory. This would be a large, interconnected series of polished mirrors and stelae covered in reflective crystal that would have two functions. If various pillars were struck simultaneously then the entire area could produce subsonic waves that could be channeled and funneled out to sea against enemy vessels. It would also have thousands of polished surfaces that could direct sunlight against enemy ships at harbor like one huge but multi-faceted magnifying gals, to set such ships afire before they could land or approach for docking.
A dyeing district, to make valuable cloth goods and perhaps also to take part in something like a silk trade. You could call it something like the Weal, or the Wister.
A industrial district, to help build inventions from the museum, and to help arm the Army and the Navy. You could call this something like the Endeavory.
A large market or bizarre (or series of them throughout the city) to help sell imported and exported items brought in by land and sea. You could name such markets after the nearby animals and products, such as the Fish Market, the Gull Market, the Bull Market, the Whale Market, the Grain Market, etc.
The Lines - these would be a series of copper or metallic lines, strung along poles in the air, or even buried underground. When stimulated with energy (such as magical force) they would vibrate and send out signals that could be received anywhere else such lines were strung. in that way imagine a city with a sister city ten miles away, or a sea-city with a garrison on an island just over the horizon. If such lines existed then they would be a sort of magical version of the telegraph. Maybe even a crude type of telephone. Unless the enemy knew what they were and how they operated you would not have to rely upon runners or horse riders to send urgent communications. And you could send message sin secret without much fear of interception or decoding.
You could achieve the same effect by building aqueduct type lines (maybe thorough an underground piping system) in which you could send written communications. Just place your message in a water tight container small enough not to jam your piping or water system and let the water flow deliver your message to the desired destination. Unless someone knew the message was being delivered in that way no one would suspect to inspect the water system for messages.
Anyway, I hope that helped.