Magnetic susceptibility (MS) and clay mineralogy data from the Bougobrine and Souar sections (middle–upper eocene) in Central Tunisia were analyzed in conjunction with existing sedimentological data to better understand the dynamics of the late eocene climate and sea-level changes. The results suggest increased activity of primary sediment sources during the late eocene, leading to significant shifts in magnetic signals and clay mineralogy. These changes began at the Uppermost Bartonian in the proximal Bougobrine section and at the base of the Priabonian in the distal Souar section. The variations in hematite, goethite, and magnetite concentrations account for MS fluctuations in the homogeneous distal shales of the Souar section. In contrast, the shallower carbonate-rich Bougobrine section shows less cyclicity, which could be linked to diagenesis, carbonate dilution, or a lack of magnetic minerals. We propose distinct sediment source regions for the Lutetian–Bartonian deposits, with contributions from the northern, eastern, and southwestern provinces. In the Priabonian, however, the increased dominance of silt and later sand (near the Eocene–Oligocene boundary) reflects a shift primarily to western and southwestern sources, with a minor contribution from the north.