Laboratory experiments have yielded evidence suggestive of large-scale meandering motions in the wake of an axial flow hydrokinetic turbine in a turbulent open channel flow (Chamorro et al., J. Fluid Mech., vol. 716, 2013, pp. 658–670). We carry out a large-eddy simulation (LES) of the experimental flow to investigate the structure of turbulence in the wake of the turbine and elucidate the mechanism that gives rise to wake meandering. All geometrical details of the turbine structure are taken into account in the simulation using the curvilinear immersed boundary LES method with wall modelling (Kang et al., Adv. Water Resour., vol. 34(1), 2011, pp. 98–113). The simulated flow fields are in good agreement with the experimental measurements and confirm the theoretical model of turbine wakes (Joukowski, Tr. Otdel. Fizich. Nauk Obshch. Lyub. Estestv., vol. 16, 1912, no. 1), yielding a near-turbine wake that consists of two layers: the tip vortex (or outer) shear layer that rotates in the same direction as the rotor; and the inner layer counter-rotating hub vortex. Analysis of the calculated instantaneous flow fields reveals that the hub vortex undergoes spiral vortex breakdown and precesses slowly in the direction opposite to the turbine rotation. The precessing vortex core remains coherent for three to four rotor diameters, expands radially outwards, and intercepts the outer shear layer at approximately the location where wake meandering is initiated. The wake meandering manifests itself in terms of an elongated region of increased turbulence kinetic energy and Reynolds shear stress across the top tip wake boundary. The interaction of the outer region of the flow with the precessing hub vortex also causes the rotational component of the wake to decay completely at approximately the location where the wake begins to meander (four rotor diameters downstream of the turbine). To further investigate the importance of turbine geometry on far-wake dynamics, we carry out LES under the same flow conditions but using actuator disk and actuator line parametrizations of the turbine. While both actuator approaches yield a meandering wake, the actuator line model yields results that are in better overall agreement with the measurements. However, comparisons between the actuator line and the turbine-resolving LES reveal significant differences. Namely, in the actuator line LES model: (i) the hub vortex does not develop spiral instability and remains stable and columnar without ever intercepting the outer shear layer; (ii) wake rotation persists for much longer distance downstream than in the turbine-resolving LES; and (iii) the level of turbulence kinetic energy within and the overall size of the far-wake meandering region are considerably smaller (this discrepancy is even more pronounced for the actuator disk LES case) compared with the turbine-resolving LES. Our results identify for the first time the instability mechanism that amplified wake meandering in the experiment of Chamorro et al., show that computational models that do not take into account the geometrical details of the turbine cannot capture such phenomena, and point to the potential significance of the near-hub rotor design as a means for suppressing the instability of the hub vortex and diminishing the extent and intensity of the far-wake meandering region.