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We present results from the archaeological analysis of 331 km2 of high-resolution airborne lidar data collected in the Upper Usumacinta River basin of Mexico and Guatemala. Multiple visualizations of the DEM and multi-spectral data from four lidar transects crossing the Classic period (AD 350–900) Maya kingdoms centered on the sites of Piedras Negras, La Mar, and Lacanja Tzeltal permitted the identification of ancient settlement and associated features of agricultural infrastructure. HDBSCAN (hierarchical density-based clustering of applications with noise) cluster analysis was applied to the distribution of ancient structures to define urban, peri-urban, sub-urban, and rural settlement zones. Interpretations of these remotely sensed data are informed by decades of ground-based archaeological survey and excavations, as well as a rich historical record drawn from inscribed stone monuments. Our results demonstrate that these neighboring kingdoms in three adjacent valleys exhibit divergent patterns of structure clustering and low-density urbanism, distributions of agricultural infrastructure, and economic practices during the Classic period. Beyond meeting basic subsistence needs, agricultural production in multiple areas permitted surpluses likely for the purposes of tribute, taxation, and marketing. More broadly, this research highlights the strengths of HDBSCAN to the archaeological study of settlement distributions when compared to more commonly applied methods of density-based cluster analysis.