There are three words in Hebrew for wall - kir קיר, choma חומה, and kotel כותל. What is the difference between them?
All three are biblical, although kotel appears only once (Shir Hashirim 2:9). Let's look at each.
Kir - this is the most common word for "wall" in Modern Hebrew. Ben Yehuda and Even-Shoshan say it might be related to kora קורה - "beam". Klein says that it is perhaps related to the Akkadian qiru and Arabic qir, both meaning asphalt, and so the original meaning may have been "something paved or painted with asphalt."
Choma is generally used to describe the protective wall around a city. Klein's etymology reflects this sense, as he derives it from the root חמה, "to see, protect". That root is common in Aramaic, and is used in the declaration made when disowning any chametz before Pesach - כל חמירא .. דחמיתה ודלא חמיתה kol chamira ... d'chamitey u'dlo chamitey - "any chametz ... that I saw or did not see".
One interesting verse that uses both kir and choma is Yehoshua 2:15
וַתּוֹרִדֵ֥ם בַּחֶ֖בֶל בְּעַ֣ד הַֽחַלּ֑וֹן כִּ֤י בֵיתָהּ֙ בְּקִ֣יר הַֽחוֹמָ֔ה וּבַֽחוֹמָ֖ה הִ֥יא יוֹשָֽׁבֶת׃
This is the New JPS translation:
She let them down by a rope through the window—for her dwelling was at the outer side of the city wall (b'kir hachoma) and she lived in the actual wall (bachoma).
That translation has kir meaning "side" and choma meaning "wall." The JPS commentary on Bamidbar 35:4 expands on this idea and writes:
Hebrew kir, a rare word for a town wall. (The term elsewhere is homah.) It probably refers to the outside surface of the town wall (see kir ha-homah in Josh. 2:15).
Artscroll adjusts the phrasing slightly - "for her house was in a wall of the fortification, and she lived in the fortification." So in this case kir means wall, and choma means fortification. This fits the explanation of Daat Mikra on Yehoshua 2:15, who writes that in order to save on construction material it was common to include houses inside the city wall, and sometimes these houses would share their walls with the city walls.
Kotel likely has Aramaic origins, and Klein points out that the Aramaic cognate כתלא kutla is probably a loan word from the Akkadian kutallu - "back side". It was used frequently in rabbinic Hebrew, but in modern Hebrew it's generally reserved to describe the western retaining wall of the Temple Mount - the kotel hamaaravi הכותל המערבי.