We map the b-value in the subduction zone of theWellington region, NewZealand, using a high quality earthquake catalogue relocated with a 3-D seismic velocity model, consisting of 50 314 events that occurred between 1990 and 2005. In order to investigate heterogeneity in the crust of the overlying plate and in the upper plane of the Wadati–Benioff Zone (WBZ), we analyse a series of cross-sections perpendicular to the strike of the subduction zone. We calculate the b-values selecting events with magnitude of completeness ≥2.4 and depth ≤65 km and projecting the seismicity within 20 km on each side of the cross-sectional planes. We observe areas of high b-value (∼1.7) near the plate interface and regions of low b-value anomalies are detected both in the WBZ in the northwest region below 40 km depth and in the overlying plate in the northern South Island at 10 km depth. The anomalies are statistically significant based on Utsu’s p-test and the bootstrap method and are not data processing method or parameter dependent. We compare the b-value distribution with previously determined 3-D distributions of Vp, Vp/Vs andQp from seismic tomography. This comparison suggests that material inhomogeneity, caused by fluid filled cracks resulting from dehydration of the subducted slab and subducted sediments, is the predominant cause of b-value variation in the shallow part of this subduction zone. Our observations are consistent with a previously proposed conceptual model that fluid distribution in the shallow part of this subduction zone is controlled by the permeability of geological terranes in the overlying plate.