River deltas grow through repeated lobe-scale avulsions, which often occur at a location that correlates with the backwater lengthscale. Competing hypotheses attribute the avulsion node origin to either the morphodynamic feedbacks caused by natural flood discharge variability (backwater hypothesis) or to the prograding delta lobe geometry (geometric hypothesis). Here, using theory, historical flood records, and remotely sensed elevation data, we analyzed five lobe-scale delta avulsions in Madagascar, captured by Landsat imagery. Avulsion lengths were 5-55 km, distances significantly longer than the backwater lengthscale and inconsistent with the geometric hypothesis. We show that the steep, silt-bedded rivers of Madagascar have flood-induced bed scour, driven by backwater hydrodynamics, that propagates farther upstream than the backwater lengthscale. The avulsion lengths are 3.1 ± 1.5 times the predicted flood scour lengths, similar to low-gradient deltas, and consistent with backwater hypothesis. Results demonstrate that erosion initiated by nonuniform flows in the backwater zone is a primary control on delta avulsion locations. Plain Language Summary River deltas grow through abrupt channel shifts, called avulsions, which pose a threat to life and property, but we do not understand why avulsions occur where they do. One hypothesis is that flood discharge variability creates a preferential zone of sediment accumulation within the so-called backwater zone of coastal rivers, which becomes the locus of avulsion. The rationale is that the flow acceleration and deceleration within the backwater zone during different sized floods creates nonoverlapping patterns of erosion and deposition resulting in a peak in sediment accumulation. If this hypothesis is correct, then avulsion sites should be farther upstream, relative to the backwater lengthscale, in steep rivers with fine-grained sediment beds that have more significant bed scour during large floods. By analyzing historical avulsions on Madagascar, we found that avulsions occurred far upstream due to the large floods and fine-grained sediment, in support of the flood discharge variability hypothesis. Our work highlights that changes in flood regime and sediment grain size of coastal rivers due to land use and climate changes can influence avulsion location.