Subaqueous vortex ripples in equilibrium are characterized by their unique geometry and dimensions. Motivated by the recent direct numerical simulation study of oscillatory turbulent flow over a wavy bottom by Önder & Yuan (J. Fluid Mech., vol. 858, 2019, pp. 264–314), the objective of this study is to further investigate the fluid dynamical controls that determine the distinctive equilibrium dimensions of vortex ripples. We use direct numerical simulations to investigate the differences in flow kinetics between sinusoidal oscillatory flow over equilibrium and out-of-equilibrium vortex ripples. In comparison with the equilibrium case, the spanwise coherent vortices, the averaged bottom shear stress on overlying flow and the shear stress distribution on the ripple surface are identified as the key fluid dynamical controls on equilibrium dimensions. Based on these controls, we propose mechanisms in the selection of vortex ripple dimensions. We observe that the flow adjusts in such a way that the interaction between overlying flow and vortex ripples tends to generate the strongest coherent vortices while the ripple surface (or overlying flow) experiences the smallest shear stress averaged over ripple wavelength during the selection process. Through a triple decomposition of the flow, the component of the ripple-induced fluctuation is found to dictate these fluid dynamical controls, which implies that this component plays an important role in the evolution of vortex ripples.