Many studies of foreland basins have recognized a hierarchical organization in the stacking of sequences deposited by axial-deltaic and alluvial fan systems. The hierarchy is often explained in terms of the competing control of eustasy and pulsed tectonic subsidence and the different frequencies at which these processes operate. Unravelling the relative contributions of tectonic and eustatic controls on the sequence stacking pattern is a fundamental question in foreland basin analysis, yet this is difficult because of the lack of independent stratigraphic evidence. In this study, a three-dimensional numerical model is presented, which aids in the interpretation of alluvial successions in foreland basins filled by transverse and axial depositional systems, under conditions of variable tectonism and eustatic sea-level change. The tectono-sedimentary model is capable of simulating the hierarchical stratigraphic response to both eustatic and tectonic forcing, and is of higher resolution than previous models of foreland basin filling. Numerical results indicate that the onset of tectonic activity is reflected by rapid retrogradation of both depositional systems and by widespread flooding and onlap of carbonate sediments. Syntectonic fluvial patterns on the axial-deltaic plain are dominated by bifurcating channels, swiftly relocating in response to the general rise in relative sea level induced by flexural subsidence. The resulting surface morphology of the axial delta is convex upwards. Syntectonic eustatic sea-level fluctuations result in parasequence-scale packages of retrograding and prograding fan and delta sediments bounded by minor flooding surfaces and type 2 sequence boundaries. Incised channels are rare within the syntectonic parasequences and are formed only during phases of tectonic quiescence when eustatic falls are no longer compensated by the subsidence component in the rise in relative sea level. Suites of amalgamating, axial channels corresponding to multiple eustatic falls delineate the resulting type 1 unconformities. Coarse-grained, incised-channel fills are found in the zone between the alluvial fan fringes and the convex-upward body of the axial delta, as the axial streams tend to migrate towards this zone of maximum accommodation.