This research aims to distinguish genetic sedimentary processes building canyon geomorphological patterns and the factors driving different sedimentary activities in two nearby Mediterranean shelf-incised submarine canyons (Carchuna and Motril) that exhibit different degrees of incision on the narrow margin of the northern Alboran Sea. The straight Carchuna Canyon incises the shelf up to 200 m off the coastline and exhibit steep canyon walls featuring narrow terraces, muddy sands with high contents of organic matter along the thalweg, and transported shelf benthic foraminifera in distal settings. The Motril Canyon head is wider and incises the shelf edge, ca. 2 km off the coastline. It exhibits a sinuous morphology and less steep walls, wider terraces, and higher sedimentation rates with muddy sediments along the thalweg. In both canyons, cross-section relief, width, incision, and area decrease downslope, although these parameters increase locally. The downslope variations of geomorphological parameters are attributed to enhanced erosional/depositional processes promoted by tectonically controlled abrupt changes of the axial channel orientation. The degree of shelf incision, the location of the canyon heads in relation with the local sediment sources, and the seasonally variable hydrodynamic regimes determine the different degrees of recent canyon activity. The Motril Canyon is interpreted as a mature system that reflects episodic activity, collecting fine-grained sediments from the nearby Guadalfeo River. The Carchuna Canyon exhibits a youthful developmental stage whose activity is more continuous and involves sediment trapping of littoral cells and continuous downslope sand transport.