The Thames Estuary was, according to the Fourth Doctor, a part of south-eastern England where the Thames emptied into the ocean.
It was once the site of an initial incursion by a single Pescaton ship. After the Doctor and Sarah discovered that a scientific expedition to the bottom of the estuary had vanished without a trace, the Doctor decided to explore. There, on the sea bed, he found the expedition party dismembered and floating lifelessly in the water. Nearby was a buried Pescaton ship, its occupants apparently elsewhere. The Doctor then surfaced so that he and Sarah could go off in search of the missing Pescaton pilot. (AUDIO: Doctor Who and the Pescatons)
Sometime in the far future, Missy and Helen Sinclair traversed the desert, where the Thames Estuary had once been, by horse. (AUDIO: Day of the Master)