Eddy resolving simulations are used to describe the mean flow and turbulence structure inside and around a square array of width D containing emerged (i.e., cylinder extending up, or above, the free surface), rigid cylinders of width d. The array is placed at the centre of a long open channel of width W. The study describes how the structure of the wake and shear layers forming along the lateral sides of the array, the wake spectral content and shedding modes, the bleeding velocity, the lengths of the steady and total wake regions, the coherence of the horseshoe vortices forming around the frontal face of the array, the bed shear stresses and the sediment entrainment capacity of the flow inside and outside the array change with the main geometrical parameters defining the array (i.e. the solid volume fraction, SVF, the non-dimensional frontal area per unit volume of the array,
$\textit{aD}$, the shape of the cylinders and
$d/D$) and the blockage ratio,
$W/D$. The effects of varying the same geometrical parameters on the total non-dimensional streamwise drag force acting on the array and on the streamwise distribution of the drag force inside the array are quantified. The mean flow and turbulence inside the array are analysed based on the streamwise distributions of the double-averaged (i.e. over time, D and the flow depth, H) streamwise velocity,
$\overline{\overline{U}}$, and turbulent kinetic energy. Contrary to wakes generated behind circular arrays of emerged cylinders, several streamwise-oriented vortices are generated inside the wake of square arrays for a limited range of
$\textit{aD}$. These vortices increase flow three-dimensionality and vertical transport behind square arrays. Despite the relatively large values of the array and channel Reynolds numbers (i.e. ReD = 40 000, ReH = 14 000), the mean (time and spanwise-averaged) cylinder drag coefficient,
${C}_{d}^{\prime}$(x), defined with d, H and
$\overline{\overline{U}}$ is not close to constant over the whole length of the array in some of the dense array simulations. In these cases,
${C}_{d}^{\prime}$ starts increasing monotonically over the downstream part of the array, as the flow transitions from the quadratic drag regime to the linear drag regime. When plotted versus the cylinder Reynolds number
$\overline{\textit{Re}_{d}} = \overline{\overline{U}}d/$ν (ν is the viscosity),
${C}_{d}^{\prime}$ = 2α0/
$\overline{\textit{Re}_{d}}$ over the linear drag regime. The parameter α0 and the critical value of
$\overline{\textit{Re}_{d}}$ corresponding to the start of the linear drag regime are strongly influenced by the main geometrical parameters of the array and the blockage ratio. Simulation results show that the close-to-constant value of the cylinder drag coefficient characterising the quadratic drag regime,
$\overline{{C}_{d}^{\prime}},$ increases with
$\textit{SVF}$ and
$\textit{aD}$ for constant
$d/D$, cylinder shape and
$W/D$. Moreover,
$\overline{{C}_{d}^{\prime}}$ increases with
$d/D$ for constant
$\textit{aD}$, cylinder shape and
$W/D$, and decreases with
$W/D$ for constant
$\textit{aD}$, cylinder shape and
$d/D$.