Current evidence suggests that Indigenous farmers in the North American Southwest began canal irrigation in the second millennium BC, marking an important change in food production technology. Early canal systems are preserved in alluvial floodplains of the US-Mexico Borderlands region, tend to be deeply buried, and can appear as natural fluvial features. Here I discuss some of the challenges in identifying early canals and associated fields and present case studies from the Santa Cruz River in southern Arizona where buried channels dating as early as 1600–1400 BC were likely human constructed. These small channels share several stratigraphic properties and are consistent with hypotheses of early canal irrigation practiced by small family groups reliant on mixed farming and foraging. Through time, irrigation canal systems expanded in size, resulting in increased labor investment, sedentism, and productivity and facilitating the development of larger irrigation communities. Stratigraphic and geomorphic properties of early canal systems thus far identified along the Santa Cruz River provide a framework for identifying potential early canal evidence in other fine-grained floodplains of the Southwest, thereby improving our understanding of Indigenous agricultural intensification.