The 23 km-diameter well-preserved Haughton impact structure shows a rather unique combination of a positive magnetic anomaly with a negative gravity anomaly over the center of its central uplift. Using a new ground magnetic dataset and several modeling approaches, we investigate the properties and geometry of its central magnetized source. Our results confirm that a km-sized magnetic body with a narrow near-surface extension is necessary to account for the anomaly. Additional measurements of rock magnetic properties of samples of all lithologies encountered in and outside the crater show that the target sedimentary rocks and the vast majority of the Precambrian basement rocks cannot be the source of the magnetic anomaly. While in larger impact structures such magnetic anomalies are often explained by magmatic mafic intrusions or highly magnetic glass lenses in the impact melt rocks, we propose that impact-generated hydrothermal activity enhanced the magnetization of the highly-porous unmelted uplifted basement rocks. Such a process may be considered for the interpretation of the geophysical signature of planetary impact craters.