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The root systems of mangroves, a tree species found in intertidal tropical and subtropical coastal zones, provide a natural barrier that dissipates wave energy effectively and reduces sediment erosion. Here, we use a combination of experiments and numerical simulations to examine the wake and drag characteristics of porous arrays of cylinders, which serve as simplified models of mangrove root networks. Optimal arrangements of the arrays are obtained by coupling Navier–Stokes simulations with a multi-objective optimization algorithm, which seeks configurations that minimize wake enstrophy and maximize drag on the porous structure. These optimal configurations are investigated using particle image velocimetry, and the internal and external flows around the porous arrays are analysed using a combination of proper orthogonal decomposition and Lagrangian particle tracking. Large variations in drag and enstrophy are observed by varying the relative positions of the cylinders, which indicates that the geometrical arrangement of porous arrays plays a prominent role in determining wake and drag characteristics. A sensitivity analysis suggests that enstrophy is more sensitive than drag to specific cylinder placement, and depends on distinctive flow patterns that develop in the interior due to interactions among neighbouring cylinders. Arrays with higher drag involve a combination of larger projected frontal area and minimal flux through the interior, leading to increased wake enstrophy, which is unfavourable for particle deposition and erosion. Based on the analysis of characteristics associated with the optimal arrays, several manually designed arrays are tested, and they display the expected behaviour with regard to drag and enstrophy.