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Large-eddy simulation was used to model turbulent atmospheric surface layer (ASL) flow over canopies composed of streamwise-aligned rows of synthetic trees of height,$$h$$, and systematically arranged to quantify the response to variable streamwise spacing,$$\delta _1$$, and spanwise spacing,$$\delta _2$$, between adjacent trees. The response to spanwise and streamwise heterogeneity has, indeed, been the topic of a sustained research effort: the former resulting in formation of Reynolds-averaged counter-rotating secondary cells, the latter associated with the$$k$$- and$$d$$-type response. No study has addressed the confluence of both, and results herein show secondary flow polarity reversal across ‘critical’ values of$$\delta _1$$and$$\delta _2$$. For$$\delta _2/\delta \lesssim 1$$and$$\gtrsim 2$$, where$$\delta$$is the flow depth, the counter-rotating secondary cells are aligned such that upwelling and downwelling, respectively, occurs above the elements. The streamwise spacing$$\delta _1$$regulates this transition, with secondary cell reversal occurring first for the largest$$k$$-type cases, as elevated turbulence production within the canopy necessitates entrainment of fluid from aloft. The results are interpreted through the lens of a benchmark prognostic closure for effective aerodynamic roughness,$$z_{0,{Eff.}} = \alpha \sigma _h$$, where$$\alpha$$is a proportionality constant and$$\sigma _h$$is height root mean square. We report$$\alpha \approx 10^{-1}$$, the value reported over many decades for a broad range of rough surfaces, for$$k$$-type cases at small$$\delta _2$$, whereas the transition to$$d$$-type arrangements necessitates larger$$\delta _2$$. Though preliminary, results highlight the non-trivial response to variation of streamwise and spanwise spacing.