Superposition!
The homes in this photo not only provide additional evidence for human occupation of the Tucson Basin in the first millennium B.C., but also serve as examples of two important principles in the study of archaeology.
The first principle is called superposition, and it is the basic logic that archaeology is founded upon. Superposition means that—usually—the stuff on top represents an earlier period of time than the stuff on the bottom. This is true for most situations—from complex and deeply layered sites like Clearwater, to more mundane circumstances like your laundry hamper.
Based on the concept of superposition, we can infer that the house on top was built much later than the house in the bottom of this pit.
The other principle that this photograph illustrates is called a natural formation process. Formation processes are what leads a site to be in the condition that it is in today. Archaeologists must account for both natural and man-made formation processes in order to interpret the past. In this case, the natural formation process that we are observing is flooding, and consequent flood deposits. Every pithouse found at the Clearwater site was filled with deposits of silt. The silt was left behind by the floodwaters of the Santa Cruz River.