Bearing in mind that Harwich is in the Thames Estuary, I assume you mean the Thames entrance?
If so... from Harwich clockwise...
Walton Backwaters - both Stone Point and Hamford Water
The Colne - Pyefleet Creek
The Blackwater - Osea Island
The Crouch/Roach - Under Foulness or just too many to mention up both rivers
If you look on Threepointfix, you'll see many of them detailed a bit further
I guess it is.... but colloquially, people assume the Thames Estuary to mean the entire coastal seaboard between The Ore and Nth Foreland in my experience