Build Like A Bridge Footing
If you have a modern urban environment and you are not going to use a dyke of some kind, probably your best option is to use what amounts to a "mini-dyke" for each major building you want to save. I say major building because you are probably not going to have the resources to save every building.
Bridges, some docks, and certain other major engineering projects use large masses of cement blown into underwater forms. There are even types of cement that can cure underwater nowadays. A bridge footing might have 10+ feet of "waterproof" cement surrounding the steel pylon that anchors part of the bridge. To really waterproof something, there will be multiple layers of different materials surrounding anything that could be corroded.
So, if we take something like a skyscraper, we might try this: We can sink extra support pylons around the skyscraper (this will be complicated because of all the service connections to things like sewers, water mains, electrical conduits, and even transportation tunnels to subways depending on the city, but since we will have to find and seal ALL of these things anyway, we might as well get to work). This will be useful to keep the building from becoming the leaning tower of Pisa when the ground underneath liquifies over time. In most cities, major buildings like skyscrapers are anchored to bedrock, but we can't count on that and there are plenty that are built on fill.
Next, we would build a containment wall in a similar way to a bridge footing all the way around the skyscraper. This wall would be probably 12+ feet thick, be made of "waterproof" cement, and have multiple layers of impermeable materials that will block water seeping in. There have been examples of walls like this being used to actually create a dry "tunnel" right down to the bottom of a harbor or bay during major construction. To save costs, we can bring the containment wall up to a reasonable height over where the water level is going to be soon. We can keep adding to the wall as the water level rises. This wall can be built as both a water "shell" and as a strongback to support the building itself if necessary, since we can expect things to get wonky once the fill dirt washes away and waves begin to beat on our structure.
If all goes well and we have a strong enough structure, we could go a ways up before we run into major trouble. Of course, the lower levels of the building will become creepy, dark, damp, mold-smelling places that nobody wants to be, and we will be constantly fighting moisture with dehumidifiers, pumps, and even mops (moisture will be inevitable, no matter what).
With any kind of large city, the problem is that there is no way to put that much effort and money into every single building in the city. In addition, smaller buildings would basically just disappear into the man made dry hole we create if the water level rises too much. We could create areas to preserve neighborhoods by making big water walls around groups of smaller buildings, but in that case, we are back to a dyke.
Basically, if you want it to last as long as you say, build it like a bridge footing.