The north Ecuador subduction zone exhibits segmentation and clustering of seismicity through megathrust, interseismic, and aftershock seismicity. In 1906, a Mw 8.8 megathrust event ruptured a 500 km segment, portions of which were re-ruptured in ’42 (Mw 7.8), ’58 (Mw 7.7), ’79 (Mw 8.2) and 2016 (Mw 7.8 Pedernales event). Segmentation between the ruptures is caused in part by subducting topography and upper plate structure. Upper plate structure in north Ecuador includes major faults, sedimentary basins and accreted terranes. An international aftershock deployment and the Ecuador permanent network (RENSIG) recorded aftershocks of the 2016 Pedernales event. We performed finite difference tomography in a joint inversion for 3D velocity and earthquake location, using body wave arrivals of aftershocks. The Manabi, Manta-Jama and Borbon sedimentary basins are observed as high Vp/Vs features with the Manabi basin seen as a low Vp and Vs feature. High Vp and Vs are associated with accreted forearc terranes. Relocation of aftershocks in the 3D velocity results in previously described “bands” of seismicity collapsing to smaller clusters ranging from ~8-40 km across. South of the rupture area, a cluster near Manabi collapsed landward, and a cluster appeared west of the trench. Three clusters between the trench and directly south of the rupture contain lower plate and plate interface events. The cluster within the rupture area between the patches of greater slip became more focused, and a cluster became defined on the north side of the northern patch of slip. Two clusters outline subducting Atacames seamounts, with events in the lower plate and interface beneath and in front of the seamounts. North of the rupture, the clusters offshore and onshore near Galera contain mostly interface with some upper plate events. The onshore cluster focused around major faults in a transition from north/south to northeast/southwest structures along the coastal range. Events in the cluster near Atacames relocated mainly in the upper plate, and events in the cluster near Esmeraldas remained in the upper plate. Interseismic events cluster in the same locations as aftershock events. Existing features including upper plate structure and subducting features control and focus both postseismic and interseismic deformation across megathrust cycles.