The study of stepped spillways in laboratory scales has been essentially focused on two separated sub-regimes within skimming flow. In this paper we investigate the appearance of an unclassified alternating skimming flow regime in a 0.5 m wide stepped spillway which does not fit on these earlier definitions, and which does not occur in a 0.3 m wide spillway. Our aim is to explain the genesis of this unclassified flow which is visualised in the physical stepped spillway, by using 3D numerical modelling. Flow depths and velocities are measured using an ultrasonic sensor and Bubble Image Velocimetry in the wider flume (0.5 m). The numerical model is validated with the experimental data from the 0.5 m wide spillway. After validation, the channel width of the same numerical model is reduced to 0.3 m wide spillway in order to characterise (compare) the case without (with) alternating skimming flow. Both cases are solved using Reynolds-Averaged Navier–Stokes equations together with the Volume-of-Fluid technique and SST k- $$\omega$$ ω turbulence model. The experimental results reveal that the alternating skimming flow regime is characterised by an evident seesaw pattern of flow properties over consecutive steps. In turn, the numerical modelling clarified that this seesaw pattern is due to the presence of a complex system of cross waves along the spillway. These cross waves are also responsible for a mass and momentum exchange in the transversal direction and for the formation of the alternating skimming flow in the spillway.