The first people here were hunter-gatherers who traversed deep canyons in terrain with few animals, limited vegetation, and scarce water. Life was difficult enough to restrict the size of their hunting groups. They supplemented game with nuts, seeds, and wild fruit. Artifacts of Paleo-Indians who camped on the Cajon Mesa date to 8,000 BC, and evidence from twenty separate sites records Archaic-Early Basketmaker people from around 6,000 BC. Those Basketmaker people earned their name: they wove baskets so skillfully they could coat them with pitch to heat water, toast seeds and nuts in them, and use them for long-term food storage. They fashioned bags, sandals, and belts from yucca leaves, strung beads, and lived in dry caves where they dug stone-lined pits to store provisions. The transition from nomadic survival to settled agriculture took thousands of years on this mesa, but when it arrived, it transformed the landscape.

By 750 AD, the Pueblo I period brought stone buildings with south-facing windows, arranged in U, E, and L shapes and clustered together in ways that reflected deepening community and religious life. Towers rose near kivas - the circular underground ceremonial chambers - likely serving as lookouts. Pottery evolved from simple cooking vessels to pitchers, ladles, bowls, and decorated dishware; white pottery with black plant-pigment designs became a distinctive craft. Water management grew sophisticated, with reservoirs and silt-retaining dams. Around 900 AD, the number of residential sites at Hovenweep increased sharply. People considered part of the Mesa Verde branch of the northern San Juan Pueblo culture transitioned from dispersed housing and built concentrated pueblos alongside springs and canyon heads. Most construction happened between 1230 and 1275, roughly the same period as the famous Mesa Verde cliff dwellings. The architecture and pottery were closely related to Mesa Verde's.

The structures that make Hovenweep distinctive are its towers. By about 1160, the inhabitants began building multi-story residential complexes - up to three stories tall - along with dams and reservoirs, moving their fields into areas where water could be controlled. They built stone towers and living quarters specifically to safeguard springs and seeps. The masonry is expert: builders adapted their designs to the uneven surfaces of natural rock slabs rather than leveling foundations. The results were so striking that 19th-century explorers called them castles. Hovenweep Castle, Hovenweep House, Square Tower, Rim Rock House, Twin Towers, and Stronghold House are the most prominent surviving structures. Each sits within a larger community pueblo surrounding a canyon head where springs emerge. The Cajon Group, at the head of Allen Canyon, held an estimated 80 to 100 people, with up to seven kiva depressions clustered around its spring and evidence of terrace farming on the talus slopes below the rim.

Hovenweep encompasses six distinct clusters of pueblo buildings, each with its own character. The Cutthroat Castle group, in an offshoot of Hovenweep Canyon, is unique because it lacks a spring - the one village that does not follow the pattern of building around water. Its numerous kivas and below-rim architecture set it apart. The Goodman Point group, the largest and easternmost village, contains pueblo buildings built partially underground, most heavily populated between 1150 and 1300 during the Pueblo III period, though Basketmakers occupied the site as early as 200 AD. Hovenweep became a National Monument in 1923. In July 2014, the International Dark-Sky Association designated it an International Dark Sky Park - a fitting honor for a place where ancient people watched the same unobstructed skies, tracking seasons by starlight to know when to plant and when to harvest. The towers still stand at canyon's edge, and after dark, the Milky Way still arches overhead exactly as it did a thousand years ago.