In all pueblo societies, language has a direct connection to religion. Language is a fluid and ever-evolving medium with a spirit of its own. The story of prehistoric history in the Southwest has to include the migration of clans and ritual specialists. As much as each has a terminology of its own, the major part of the languaging used in their rituals is derived from Keres. All the pueblos are also congregations of different clans, some even from non-pueblo tribes.
The languages have been traced back to a postulated "Amerind" tongue spoken by many people across the Americas. Zuni and Uto-Aztecan are descendants of that, both branching about the same time. Zuni, however, stayed in one region while Uto-Aztecan spread across the Southwest and onto the southern Plains. It's only later that Keres, Towa and Tewa diverged and later yet that Tiwa diverged. We don't know about Piro or Tompiro as the speakers of those languages all died out after the introduction of European religion and disease. We don't know anything about the Mogollon language either as those people melted into other societies in the 1400s. Hopi is a polyglot of multiple Uto-Aztecan variants, including some Zuni as the people of the various groups across the southwest sometimes congregated around Hopi or were sometimes visited by long-term delegations from Hopi.
More recently, it wasn't until it became clear to tribal elders that their language was dying before they would allow the creation of a written version or a dictionary of their language as part of the efforts to preserve their language(s). The people of Jemez still forbid any written forms of their language and that stops development of a Towa Dictionary... and the people of Jemez are the only speakers of Towa.
Pecos Pueblo (Cicuye) is reputed to have spoken Towa but there is also evidence Cicuyé was a Tewa pueblo that absorbed a large group of Towa people at a time when they needed it. When Cicuyé was finally abandoned in 1838, the last few residents were invited to move to Jemez and they did so. They do still return to the site of Cicuyé every year for certain religious ceremonies and to honor their ancestors.
Native languages spoken among the pueblos are Hopi, Zuni, Keres, Tiwa, Tewa and Towa. Many Hopi and Hopi-Tewa also speak Navajo. While many also speak Spanish, there are still a few in the Southwest who have never learned to speak English.
Zuni has been classed as a complete "isolate" (meaning: isolated so long it has developed along its own path without traceable root). It has recently been postulated that Zuni is an offshoot of an "Amerind" language family that also branched into Uto-Aztecan. The Zuni language, though, developed and stayed in one location while the other offshoots migrated across the landscape for thousands of years. However, when it comes to religion, the Zunis share many words with the Hopis, the Keresans and the Pimas (from down south in Arizona - descendants of the Hohokam). Zuni also has a long history of being a multi-ethnic community with close ties to other multi-ethnic communities.
Hopi is classed as a member of the Uto-Aztecan family, a group of languages that span from central Mexico to Oregon and Idaho. Hopi, as a language, varies depending on which village we're talking about. The Hopi spoken at Walpi has significantly more words of Tewa, Towa, Zuni and Keres derivation than the Hopi spoken at Oraibi. And then there's the Hopi spoken at Sichomovi, the Zuni pueblo on Second Mesa. It's not just a matter of dialects either: Hopi has also long been a grouping of multi-ethnic communities.
Keres is also classed as an isolate and the two main branches, Eastern and Western, are sometimes classed as separate languages. However, many Keresan words around religion, kiva practices and clan societies are shared among Hopi, Zuni and all the Rio Grande pueblos. The two branches diverged about 1,000 years ago when they split apart in the Four Corners area and went in different directions.
Due to terminology injected from Plains tribe sources, Tiwa, Tewa and Towa have been grouped in the Tanoan-Kiowa family of languages. In the Tanoan-Kiowa group, Towa is closer to Kiowa than to Tewa-Tiwa but all tongues in the group share a common ancestor. A proposal has been put forth that would convert the Tanoan-Kiowa family to a Tanoan-Aztecan family with a connection to the Uto-Aztecan family and the greater overview that would create would potentially bring the Zuni language into connection with an "Amerind" proto-language.
Further research indicates that proto-Keresan was most likely spoken in the Chaco Canyon and Aztec areas. It went straight from Chaco to Acoma and Laguna early but didn't make it to the middle Rio Grande for another 5 or 6 hundred years. That would account for differences between Eastern (Santo Domingo/Kewa, Cochiti, San Felipe, Santa Ana and Zia) and Western Keres (Acoma and Laguna).
It also appears that Keres was the language of choice through most of the Mesa Verde area in the 1200s and made its way down to the Rio Grande via the San Juan River, Gobernador Canyon and the Jemez River.
Proto-Tewa/Tiwa seems to have sourced from the Upper San Juan River area, although I've had a Tewa elder tell me there was significant time spent in the area of Yucca House, west of Mesa Verde. In any event, proto-Tewa/Tiwa pushed into the Tewa Basin (where San Ildefonso, Santa Clara, Tesuque, Nambe, Pojoaque and Ohkay Owingeh are now) from the Rio Chama and Pajarito Plateau areas. They either displaced or merged with the indigenous hunter-gatherer societies who spoke Tanoan-Kiowa language descendants and had occupied the area up to that point. Last ones down out of the mountains were forced to leapfrog over Tewa Basin and go to the Pot Creek area. Others who went south occupied the Middle Rio Grande where Coronado found them in 1539-40. The gap between the Taos area and the Middle Rio Grande caused the fracture into Northern and Southern Tiwa.
The first proto-Northern Tiwa settlement was at Pot Creek Pueblo. That is where they first mixed with the indigenous people the Spanish later named Xicarilla. That's a possibility of where the Tiwa language began to really diverge into Northern and Southern branches as the Northern branch began to include some Jicarilla terminology. When Pot Creek Pueblo burned and was abandoned in 1275, the Northern Tiwa scattered, mostly to Taos and Picuris.
The Southern Tiwa occupied the area from the Jemez River southward along the Rio Grande to around San Lorenzo. When Coronado first appeared in the area in 1540, he found "12 or 13 large pueblos" in the area. When Don Juan de Oñaté came through in 1598, that had been reduced by European diseases to 2 still-living pueblos: Isleta and Alameda (now known as Sandia).
The Towa story is a bit different. There is a long history of Towa being spoken in the areas east of the Hopi mesas, one being Antelope Mesa. Archaeologists have said the Towa moved east from Tusayan around 1000 CE, building stone towers and pueblos as they went. They maintained contact and trade with their cousins in Tusayan over the years, up until the Spanish first entered their villages in the Jemez and began preaching their religion. The first Spanish mission in Hopiland was built at Awatovi, a large Towa-speaking pueblo on Antelope Mesa, in 1629. The mission was partially destroyed in the Pueblo Revolt of 1680 and its relics scattered among the townspeople. When the Spanish priests and militia returned in 1698, they rebuilt the mission, put the relics back in place and tried to continue with business as usual. However, other Hopis banded together and destroyed Awatovi in early 1701, possibly because of that Christian presence. After that, though, the Towas of Jemez maintained closer ties with the Navajos of Jeddito.
The Piro lived in the Rio Grande Valley south of Isleta and the Tompiro lived east of the Manzano Mountains, southeast of Isleta. The Tompiro survived long enough to build missions to the Fransciscan God, then they succumbed to the diseases His missionaries brought. Those Piros who weren't killed outright by the Spanish in 1680 as they retreated southward, were likely killed by northern warriors escorting the Spanish south. The northern warriors assumed the Piros and any Isletans they met along the way were Spanish collaborators and, like the hated Spanish had done for years, the warriors killed them immediately.