A scour hole in the pre-excavated plunge pool bed downstream of a dam can develop if the energy dissipation of the plunging jet from a spillway is underestimated. The objective of the research was to predict the equilibrium geometry of the scour hole downstream of a high-head dam to safeguard the stability of the dam foundation. A study incorporating both physical and numerical modeling was undertaken to examine the hydrodynamic and geo-mechanical aspects involved in rock scour. Experimental tests were performed to determine equilibrium scour hole profiles in an open-ended, jointed, movable rock bed under various conditions, including different flow rates, dam heights, plunge pool depths, rock sizes, and joint structure orientations. Based on the experimental findings, non-dimensional equations that describe the scour hole geometry were developed. The proposed innovative three-dimensional fluid–solid coupled numerical model is capable of realistically reproducing the equilibrium scour hole profile observed in the experimental tests. The numerical model allows detailed scour computations of fully developed rectangular jets plunging into shallow plunge pools.