Crustal heat loss processes in contexts other than mid-ocean ridge flanks are still poorly understood and described in the literature. In this work, we present 54 new surface heat flow measurements recorded along the South Balearic margin and across the Hannibal High area, in the Western Mediterranean Sea, away from spreading centres. The South Balearic margin is a narrow continental margin expressed on the seabed topography by the steep Emile Baudot Escarpment while the Hannibal High area, further south, is a presumed volcanic oceanic crust zone. Recent heat flow studies pointed out the presence of strong local thermal anomalies, imprinted in regional deep basin heat flow increasing from the eastern to the western Algerian basins (70–90 to 100–130 mW/m2). The new data in this study confirm local anomalies around the Emile Baudot seamounts and allow the delineation of some low and high heat zones. We show that (1) a correlation exists between the heat flow variability and the sedimentary cover thickness, and (2) the most pronounced anomaly is a low heat flow zone (30 km wide) observed in the mid-slope South Formentera basin, close to the basaltic basement of the Los Martines volcano. The correlation of heat flow with sedimentary thickness, the lateral extent of the heat flow anomalies, the flux peak magnitudes, and the co-existence of both low and high anomalies suggest the presence of an active fluid circulation system. Based on the arrangement of the anomalies in relation to the basaltic basement seamounts, we consider a syphon-type circulation system in the Formentera basin. Reduced heat flow suggests a recharge zone close to the Los Martines seamount, while local high heat flow located close to a smaller seamount could be a potential zone of fluid discharge. Although different buoyancy-driven circulations could occur in the South Balearic margin, we believe that a syphon-type hydrothermal circulation along permeable basaltic mounds and sealed basement conduits, similar to the off-axis oceanic crust, is best developed in the young marginal basin of the South Balearic margin.