Abstract <p>To reveal the statistical characteristics of lateral vortex structures in open-channel turbulence over a non-uniform rough bed, seven sets of open-channel experiments were conducted using particle image velocimetry. The rough bed was formed by staggered cubes of two distinct sizes. The Reynolds number <i>Re</i> ranged from 4736 to 11,839. Based on experimental data, the spatial distribution and statistical properties of lateral vortex structures in the longitudinal section were analyzed. The results showed that a shear layer formed near the cube tops. In this region, prograde vortices were characterized by high density, large size, and strong rotational intensity, whereas retrograde vortices exhibited the opposite trend. In the upper flow region away from the cubes, the density of prograde vortices decreases with distance from the bed, while the density of retrograde vortices increases. The rotation intensity of both types decreases toward the free surface. In this region, the relative submergence <i>h</i>/<i>D</i> strongly affects all statistical vortex parameters. The friction Reynolds number <i>Re</i>_<i>τ</i> appears to influence only the rotation intensity. Suitable scaling relations were obtained for the dependence of vortex density and radius on <i>h</i>/<i>D</i>, and for the dependence of rotation intensity on <i>Re</i>_<i>τ</i>. Prograde vortices contribute up to 35% to the Reynolds stress, while retrograde vortices contribute about 6%. Near the sidewall, the contribution of retrograde vortices can reach 20%. Linear stochastic estimation revealed linearly aligned vortical structures with an inclined orientation near the cubes, with larger structures observed near the large cube.</p> Graphical abstract <p></p>