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Turbulent shear flows are abundant in geophysical and astrophysical systems and in engineering-technology applications. They are often riddled with large-scale secondary flows that drastically modify the characteristics of the primary stream, preventing or enhancing mixing, mass and heat transfer. Using experiments and numerical simulations, we study the possibility of modifying these secondary flows by using superhydrophobic surface treatments that reduce the local shear. We focus on the canonical problem of Taylor–Couette flow, the flow between two coaxial and independently rotating cylinders, which has robust secondary structures called Taylor rolls that persist even at significant levels of turbulence. We generate these structures by rotating only the inner cylinder of the system, and show that an axially spaced superhydrophobic treatment can weaken the rolls through a mismatching surface heterogeneity, as long as the roll size can be fixed. The minimum hydrophobicity of the treatment required for this flow control is rationalized, and its effectiveness beyond the Reynolds numbers studied here is also discussed.