We study the dynamics of turbulent boundary layer flow over a heterogeneous topography composed of roughness patches exhibiting relatively high and low correlation in the streamwise and spanwise directions, respectively (i.e. the roughness appears as streamwise-aligned ‘strips’). It has been reported that such roughness induces a spanwise-wall normal mean secondary flow in the form of mean streamwise vorticity associated with counter-rotating boundary-layer-scale circulations. Here, we demonstrate that this mean secondary flow is Prandtl’s secondary flow of the second kind, both driven and sustained by spatial gradients in the Reynolds-stress components, which cause a subsequent imbalance between production and dissipation of turbulent kinetic energy that necessitates secondary advective velocities. In reaching this conclusion, we study (i) secondary circulations due to spatial gradients of turbulent kinetic energy, and (ii) the production budgets of mean streamwise vorticity by gradients of the Reynolds stresses. We attribute the secondary flow phenomena to extreme peaks of surface stress on the relatively high-roughness regions and associated elevated turbulence production in the fluid immediately above. An optimized state is attained by entrainment of fluid exhibiting the lowest turbulent stresses – from above – and subsequent lateral ejection in order to preserve conservation of mass.