This list is far from complete.
There is not always an 1:1 relation between a place etc. in Roman times and a name in our days.
Sometimes a people giving their name to a place and that place are combined.
Some names are followed by a link to a site with that title
I tried to find suitable sites in English, but did not always succeed.
If you know better sites, please let me know.

Adrana(1) Albudignus(1) Auha(1) Cambyses(1) Clitumnus(1) Corma(1) Curtius(1) Cyrus(1) Danube(29) / Danuvius(0) / Donau(0) / Hister(2) / Ister(2) / Istrus(0) Doubs(1) Eufrath(0) / Euphrates(27) Exampaeus(1) Flutausis(1) Gilpil(1) Grisia(1) Iatrus(1) Jordan(12) Jordan Valley(0) Margus(1) Maritsa(0) / Hebrus(1) / Marisia(1) Meuse(8) / Maas(0) / Mosa(4) Miliare(1) Nile(10) / Nilus(0) Numicius(5) / Numician(0) Pagyda(1) Panda(1) Phlegeton(0) Potamus(1) Rhine(119) / Rhein(0) / Rhenus(0) Sarnus(1) Save(0) / Savus(1) Sindes(1) Tigris(5) Ulbius(1)