RobA, I had a chance to correspond with Roger Porter about a year ago when he was working on a similar project. I pointed him to this site and I hope he'll show and be able to give you some pointers. His finished piece is at http://www.diamondthrone.com/resourc...cs/Ka_Rone.jpg I suspect Ka Rone is a wee bit too symmetric and planned for what you want to do (it was a Giant city created for the Arcana Unearthed setting), but it may give you a few ideas you want to use in drawing your city.
Turning to the real world, there are three locations I would check out: Venice, Amsterdam, and the canals of Southern England (although the last are a bit anachronistic having been built in the 18th and 19th centuries).
I would keep several things in mind as you constructed your city. One: if your city is like Venice (which was built on several islands close to each other) then it will have many canals, if the canals were dug, the system is not likely to be as extensive (although magic might be used to overcome it, the lack of modern construction equipment will impose limits on how extensive the canal system can be).
Two: markets, taverns, warehouses and other commercial establishments will cluster near the port areas and the grand canals (as with a road grid, while there may be many roads, there are only a very few that carry the bulk of the riverine and walking traffic). There should be plazas/open spaces near the ports as these can function as open air markets and the sheer amount of traffic congestion caused by a port needs an open space to relieve it.
Three: houses will tend to be 3-5 stories and face inward toward a courtyard in a Venice like city since the canal system is also functioning as a sewer system (although they're trying to clean the canals up, Venice is only now beginning to tackle this problem--if you ever visit, don't do it in the height of the summer as the stench you may never forget . Given the stench (unless the city somehow uses magic to clean the canals) no one in their right mind will want windows at ground level and the higher elevation can be conducive to catching breezes (which along with fans were the only type of air conditioning in the middle ages).
Four: keep in mind the riverine port will be handling shallow draft ships while the ocean port will be handling deep draft ships (thus the ocean port might have drydocks for keelhauling and construction while the riverine port will have the terminus of towpaths for donkeys/horses to drag the boats back upstream). One excellent example of a interior riverine port (no canals though) was Salzburg in Austria which became very wealthy handling salt from the mountains upstream. Speaking of wealth, there should be nicer neighborhoods in your city as all the wealth flowing through it is likely to generate a decent sized merchant class.
Five: Last, but not least, while a canal city is likely to have many bridges, most of them will be wood. While magic can change things, the lack of steam power and heavy duty machines made constructing stone bridges expensive and a long term project (similar to building the Hoover Dam today--environmental considerations aside, the sheer expense of that type of project is going to mean that it gets built very, very rarely). As a real world example (and I would appreciate any Britons correcting me if this is wrong) London Bridge was the only bridge that crossed the lower Thames for centuries. It wasn't until the Renaissance and more recent times that more spans started being thrown across. Also, given the importance of stone structures and the scarcity of space in cities, like the original London Bridge it is not unusual for a stone bridge to be a miniature community in itself with structures built/hanging on the sides--sometimes completely blocking the view of the river!
I hope the above provides a little bit of help. Good luck with mapping out your city. I hope you post it online when done.