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 Russian темно (Proto-Slavic *tьmьnъ), 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 Indo-European but pre-Celtic and has a name indicating "muddiness" from a root *tā-, 'melt'. It has also been suggested that it is not of Celtic origin, but Germanic (thus linking it with the Eem, Ems and Amstel rivers) meaning: "inhabited place where the estuary begins", i.e. a place by the river, rather than the necessarily the river itself.

The river's name has always been pronounced with a simple t /t/; the Middle English spelling was typically Temese and Celtic Tamesis. A similar spelling from this era (AD 1210), "Tamisiam", is found in Magna Carta. 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, from where early Celtic tribes were wrongly thought to have migrated to Britain.

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 called the River Isis. Historically, and especially in Victorian times, gazetteers and cartographers insisted that the entire river was correctly named the 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 outside of Oxford, and some historians suggest the name Isis is nothing more than a truncation of Tamesis, the Latin 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. An alternative, and simpler proposal, is that London may also be a Germanic word: as "Landen" with a similar origin to the word "land".

Tamese was referred to as a place, not a river in the Ravenna Cosmography.