Etymology
The Thames, from Middle English Temese, is derived from the Celtic name for the river, Tamesas (from *tamēssa), recorded in Latin as Tamesis and yielding modern Welsh Tafwys "Thames". The name probably meant "dark" and can be compared to other cognates such as Sanskrit tamas, Irish teimheal and Welsh tywyll "darkness" (Proto-Celtic *temeslos) and Middle Irish teimen "dark grey", though Richard Coates mentions other theories: Kenneth Jackson's that it is non Indo-European (and of unknown meaning), and Peter Kitson's that it is IE but pre-Celtic, and has a name indicating muddiness from a root *tã-, 'melt'.
Note also other river names such as Teme, Tavy, Teviot, Teifi (cf Tafwys).
The river's name has always been pronounced with a simple t /t/; the Middle English spelling was typically Temese and Celtic Tamesis. The th spelling lends an air of Greek to the name and was added during the Renaissance, possibly to reflect or support a claim that the name was derived from River Thyamis in the Epirus region of Greece, whence early Celtic tribes were erroneously thought to have migrated.
Indirect evidence for the antiquity of the name 'Thames' is provided by a Roman potsherd found at Oxford, bearing the inscription Tamesubugus fecit (Tamesubugus made this). It is believed that Tamesubugus' name was derived from that of the river.
The Thames through Oxford is sometimes given the name the River Isis. Historically, and especially in Victorian times, gazetteers and cartographers insisted that the entire river was correctly named the River Isis from its source down to Dorchester-on-Thames, and that only from this point, where the river meets the River Thame and becomes the "Thame-isis" (supposedly subsequently abbreviated to Thames) should it be so called. Ordnance Survey maps still label the Thames as "River Thames or Isis" down to Dorchester. However since the early 20th century this distinction has been lost in common usage even in Oxford, and some historians suggest the name Isis—although possibly named after the Egyptian goddess of that name—is nothing more than a contraction of Tamesis, the Latin (or pre-Roman Celtic) name for the Thames.
Richard Coates suggests that while the river was as a whole called the Thames, part of it, where it was too wide to ford, was called *(p)lowonida. This gave the name to a settlement on its banks, which became known as Londinium, from the Indo-European roots *pleu- "flow" and *-nedi "river" meaning something like the flowing river or the wide flowing unfordable river.
Tamese was referred to as a place, not a river in the Ravenna Cosmography.
For merchant seamen, the Thames has long been just 'the London River'. Londoners often refer to it simply as 'the river', in expressions such as 'south of the river'.
Read more about this topic: River Thames
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