Clercon, I like your maps. I have little doubt it will be a stunner when complete. I did have a few questions/observations from a realism point of view you might want to keep in mind as you draw your map:
The first question that comes to mind--what's the scale? Are these two cities a mile or two apart or are they 20 miles apart?
Second, if the cities are less than a mile or two apart, why is the canal between them so wavy? If the canal is man made, then it would likely have been dug as straight as possible, the only reason it would be that wavy was if the landform and terrain required it (which to be honest, is the explanation you might want to run with--your canal looks far more "interesting" than a straight line would be).
Third, where are the locks? Although the two bodies of water on either side of Ankh Bator are likely close to the same height (for example at the Panama Canal, the Pacific is 20 cm higher than the Atlantic or about 8 inches), locks would facilitate two way traffic by moderating or eliminating a strong current and enabling horses, donkeys or whatever tow system you want to rig up to tow the ships from end to end (lookup the Erie Canal), they also can slow, moderate, or stop a storm surge from wiping out everything along the canal.
Fourth, and this point ties into question two, is this piece of land the continental divide between two or more tectonic plates? I know it sounds a bit over the top, but Panama is, which is why it is so mountainous. If that is the case with Ankh Bator, the central part of the canal would be higher than either end. You'd just need to find a source of water to keep the canal running (Panama's is the massive amount of rainfall (69 inches a year) that keeps Gatun Lake filled). Perhaps there is some massive dwarven waterworks, aqueduct or similar system--just the thing requiring hardy adventurers when it starts developing problems.....
Fifth, and I know this is early in the process, the canal will likely have towpaths on either side (or at least one side). There should also be markets. One final consideration is defense. Although the city is in the middle of a powerful nation If I remember your first reference to it correctly, what is to keep raiders attacking either on land or sea? City walls may not be necessary if the land the city is in has been at peace for a long time, but there should be at least some sea forts to deal with the marauding riff raff.
Regardless, I'm curious to see how this develops. Good luck.