Studies have shown the importance of submarine canyons as conduits of land-derived organic carbon beyond the coastal shelf into the deep-sea where a single obvious river source can be identified. When there is more than one river source, identifying which rivers contribute to canyon sediment organic matter is technically challenging. Here, we compare two contrasting submarine canyons: the Hokitika Canyon, a long, narrow, and gently sloping canyon on the west coast of New Zealand; and the Kaikōura Canyon, a high productivity, short, steep canyon close to shore on the east coast of New Zealand. Both canyons have multiple potential river sources, so we applied a compound specific stable isotope (CSSI) tracking technique to identify and apportion the contribution from each river at locations along the length of each canyon axis. We found that land-derived organic matter contributed between 74 and 100% of the total organic matter in the sediment of the Hokitika Canyon as far as 200 km from shore and to depths of 2000 m. However, less than 50% of the land-derived organic carbon came from the largest river closest to the canyon head. We hypothesize that longshore drift transported much of the sediment from that river past the Hokitika Canyon, while river inflows farther up-current supplied the bulk of the land-derived organic carbon. In contrast, land-derived organic matter contributed less than 50% of the total organic matter in Kaikōura Canyon sediments with land-derived organic sediment contribution decreasing steeply to less than 15% at about 24 km from shore in 1500 m water depth. Most of the land-derived organic matter (ca. 80%) came from the river with the largest suspended sediment yield, despite another (smaller) river discharging closer to the canyon head. We hypothesize that this difference in carbon source is partly due to