The River Thames can first be identified as a discrete drainage line as early as 58 million years ago, in the late Palaeocene Period Thanetian Stage. Until around half a million years ago, the Thames flowed on its existing course through what is now Oxfordshire, before turning to the north east through Hertfordshire and East Anglia and reaching the North Sea near Ipswich. At this time the river system headwaters lay in the English West Midlands and may, at times, have received drainage from the North Wales Berwyn Mountains. Arrival of an ice sheet in the Quaternary Ice Age, about 450,000 years ago, dammed the river in Hertfordshire and caused it to be diverted onto its present course through London. This created a new river route aligned through Berkshire and on into London after which the river rejoined its original course in southern Essex, near the present River Blackwater estuary. Here it entered a substantial freshwater lake in the southern North Sea basin. The overspill of this lake caused the formation of the Dover Straits or Pas-de-Calais gap between Britain and France. Subsequent development led to the continuation of the course which the river follows at the present day.
At the height of the last ice age around 12000 years ago, Britain was connected to mainland Europe via a large expanse of land known as Doggerland in the southern North Sea basin. At this time, the Thames' course did not continue to Doggerland, but was aligned southwards from the eastern Essex coast where it met the Rhine, the Meuse and the Scheldt flowing from what are now The Netherlands and Belgium. These rivers formed a single river—the Channel River (Fleuve Manche)—that passed through the Dover Strait and drained into the Atlantic Ocean in the western English Channel.
Various species of bird feed off the river or nest on it, some being found both at sea and inland. These include Cormorant, Black-headed Gull, and Herring Gull. The Swan is a familiar sight on the river but the Black Swan is more rare. The annual ceremony of Swan upping is an old tradition of counting stocks. Geese that can be seen include Canada Geese, Egyptian Geese, and Bar-headed Geese, and familiar ducks include the Mallard, Mandarin Duck, and Wood Duck. Other water birds to be found on the Thames include the Great Crested Grebe, Coot, Moorhen, Heron, and Kingfisher. In addition there are many types of British birds that live alongside the river, although they are not specific to the river habitat.
The Thames contains both seawater and freshwater, thus providing support for seawater and freshwater fish. The salmon, which inhabits both environments has been reintroduced, and succession of fish ladders built into weirs to allow them to travel upstream. The eel is a particularly associated with the Thames and there were formerly many eel traps designed to catch them. Some of the freshwater fish to be found in the Thames and its tributaries include brown trout, chub, dace, roach, barbel, perch, pike, bleak, and flounder.
In addition the Thames is host to some invasive crustaceans including Signal crayfish and Chinese Mitten Crab.
On January 20, 2006, a northern 16-18 ft (5 m) bottle-nosed whale was spotted in the Thames and was seen as far upstream as Chelsea. This is extremely unusual because this type of whale is generally found in deep sea waters. Crowds gathered along the riverbanks to witness the extraordinary spectacle. But it soon became clear there was cause for concern, as the animal came within yards of the banks, almost beaching, and crashed into an empty boat causing slight bleeding. Approx. 12 hours later, the whale was believed to be seen again near Greenwich, possibly heading back to sea. There was a rescue attempt lasting several hours, but it eventually died on a barge.