Look at real cities and use them as a guide. Something I do is a time line map, it is not detailed and very rough.
First start with the founding of the site - it is on a river, is it a safe harbor? If yes (and it should be) that means it is important, a fort would be built to protect it, a light house added.
Now, start building from the waters edge - first you would have docks, then warehouses, the tavens and homes for the dock workers. Merchants and the rich would want to be off the flood plain.
Start thinking about the boom times - maybe a new fort is needed, one is created a little up the river. The road to it starts to build up with inns and taverns for the men there. Next the area between starts to fill in.
Now the gangs - fishermen and dock workers have issues, it is space on the docks. Someone steps in and takes control, the fishermen decide that they need a dock of their own and build away from the other. This has created a line in the sand, that side dock workers, this one fishers. This can be done for each area as based on nature, rich, poor, fishers, dockers, merchant, anything else.
