I just now discovered that a piece of shoreline outside the Imperial City is missing. It's not the end of the world, but it bugs me a little. My question, then, is how I would go about tracking down which mod is causing this. I'm sure there's already been plenty written about such things, so even a link to point me in the right direction would be appreciated. Thanks.

deactivate mods one at a time till the problem goes away, then you will know which mod caused the problem

Do you have Wrye Bash? Is the Bashed Patch built correctly? It sounds like conflicting water height or landscape settings. You can try Land Magic - http://www.tesnexus.com/downloads/file.php?id=30519 <-- but take care of the Bashed Patch first, if you have one

Does the hole not go away when you restart the game?

I'm not using Wrye Bash and the 'hole' does persist through restarts. I'll start a clean game and enable mods one by one until the problem duplicates, I suppose.

Have you tried running TES4LODGEN?