This problem was reported earlier (http://forum.simutrans.com/index.php?topic=3409.msg39862#msg39862) and apparently got fixed (http://forum.simutrans.com/index.php?topic=3409.msg46417#msg46417), but I've just downloaded Experimental 9.2 and Britain pak 0.7.1 (http://forum.simutrans.com/index.php?topic=6436.msg61905#msg61905) and can't build a shipyard on a canal, therefore can't run any canal transport.
No such problem in Standard edition.
Shipyards can be built on canals, but, like all depots built on a linear way (such as a road or railway), they need to be built at the end of that way (in other words, on a dead-end stretch of canal), rather than in the middle of it.
Ah, silly me. I thought that was what I was trying to do, but I was expanding un-navigable stream into canal, and didn't notice I was trying place a shipyard with a small stream running through the backyard :palm: