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I was working off this, from the Canal Museum:
London Canal Museum adopts the convention of using "Lee" when referring to the navigation, and "Lea" when referring to the natural river. The waterway is a natural river that has been greatly improved by man over the centuries, and sections of it are entirely man-made canal. It is a bit of each, therefore, and we generally refer to it as a navigation
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Obviously, that's a convention one can adopt, but it's fairly arbitrary, e.g. with respect to spelling. I was told by a local historian and land use campaigner who really knew her area that the 'Lee' spelling was the one traditionally used in Essex and the 'Lea' spelling in Middlesex. I've always trusted that and have never checked it. Again, obviously, it's hardly important enough not to be re-purposeable.
The 'navigation' bit I don't think makes much sense. The Thames is also canalised for a long stretch in Central London, but you don't refer to it as the 'Thames Navigation'. True, the Lea doesn't have its original course on the stretch in question (heavily engineered for the reservoirs), but neither does the Rhine for most of the Upper Rhine Valley, and again nobody calls it a different name for that. The Lea has one course before it splits just south of Lea Bridge, where they decided to leave it in much of its original course and additionally build the Lea Navigation that's straight as an arrow.
Well, 'e' is associated with one county, 'a' with the other.
That it's not the you-know-what there is not controversial at all, though. It is you-know-what-ed, but it the river.