A near-bottom geophysical survey on the Endeavour segment of the northern Juan de Fuca Ridge shows that regions of well-defined low crustal magnetization are strongly correlated with both active and extinct submarine hydrothermal vent sites. In particular, at the Main Endeavour Field, we find discrete magnetization lows associated with each cluster of vents. Magnetization lows are directly centered beneath the vent clusters and have diameters of ∼100 m, which implies a near-vertical, narrow, pipe-like source region located directly beneath the surface expression of the vent edifices. Lows are also separated from each other by only 200 m, which further implies highly focused zones. Magnetization lows are also associated with inactive and extinct vent areas, which indicates that alteration of the magnetic minerals in the crust rather than (necessarily temporary) thermal demagnetization is the primary process responsible for the low magnetization. These narrow pipe-like bodies are highly characteristic of alteration pipes found in ophiolites and are indicative of hydrothermal fluid up-flow zones. Thus, each magnetization low may define an individual upwelling zone, with distinct subsurface plumbing and thermal structure. The crustal-magnetization patterns provide important constraints on the geometry of the subsurface plumbing beneath these hydrothermal vent systems. At the Main Endeavour Field, magnetization lows are distributed along the trend of the rift valley in a semiregular pattern with a spacing of ∼200 m, arguing that upward flow may be partitioned into regularly spaced intervals along the axis of the rift valley.