This article explores a means used by Byzantine agriculturists in the Negev in southern Israel to achieve sustainable soil improvement: pigeon manure. We found high concentrations of manure in ancient pigeon towers strewn across the Byzantine agricultural landscape, characterized by the widespread construction of terraces and dams to manage runoff and floodwater. We show that nitrogen (N), phosphate (P) and organic matter (OM), reliable and recognized indices of soil characterization used by both practical agriculturists and archaeologists, are associated with such towers. The distribution patterns of these indicators have shown congruent and significant perturbations north of the pigeon tower at Shivta. Comparisons with other ancient Levantine installations of this type suggest that the perturbations we identified are associated with a single, above-ground opening that did not survive the destruction of the tower. The door facilitated the controlled, periodical extraction of accumulated manure from inside the tower. This study supports the suggested importance of pigeon manure, evidently used to ameliorate local desert soils, and stresses the usefulness of chemical tests, traditional quantifiers of agricultural soil quality, and anthropogenic interference in identifying pigeon towers and clarifying archaeological problems in a desert environment.