A non-invasive investigation, integrating aerial photography and high-resolution magnetic survey, was carried out at the Masseria Pantano site (Apulia, Southern Italy) to obtain a more detailed reconstruction of an extensive ancient settlement, which revealed different phases of human frequentation. The results of the ground-based survey were also used to guide some archaeological excavations, which brought to light, mainly, parts of Medieval wall and column foundations. The correlation between the magnetic anomalies and archaeological remains was very satisfying, except for the lack of a source body that could explain the origin of a positive anomaly, the intensity and extent of which is very significant. A supplementary magnetic survey combined with stratigraphic interpretation from two boreholes, followed by susceptibility measurements, were able to solve this interesting partial misunderstanding between archaeological and magnetic data. This approach revealed clear evidence for a canal, probably Roman in date, which lies beneath the presumed ancient surface identified during the excavation.