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Abstract The mechanisms controlling transport and retention of microplastics (MPs) in riverine systems are not understood well. We investigated the impact of large roughness elements (LREs) on in-stream transport and retention of the ubiquitous polystyrene-microplastics (PS-MPs). Scaled experiments were conducted with and without LREs under various shear Reynolds numbers (Re*) in an ecohydraulics flume. Our results, for the first time, demonstrated a clear dependence of the MPs’ velocity onRe*in LREs-dominated channel. Two distinct regimes and thresholds were identified: lowerRe*(≤ 15,000) regime corresponding to higher velocities of MPs ($${U}_{MPs}^{*}$$ $U_{\mathrm{MPs}}^{\ast }$> 0.45), and higherRe*(> 15,000) to lower$${U}_{MPs}^{*} ($$ $U_{\mathrm{MPs}}^{\ast }($< 0.45). The presence and higher density of LREs increasedRe*, decreased$${U}_{MPs}^{*}$$ $U_{\mathrm{MPs}}^{\ast }$, and enhanced the PS-MPs capture. The LREs-generated turbulence kinetic energy (TKE) was found to be a good predictor of PS-MPs transport and retention rates, indicating the effectiveness of LREs in retaining PS-MPs in streams and rivers.