Cyanobacterial harmful algal blooms and microcystins (MCs) pollution pose serious threat to aquatic ecosystem and public health. Planted and unplanted constructed wetlands (CWs) filled with four substrates (i.e., gravel (G-CWs), ceramsite (C-CWs), iron-carbon (I-CWs) and slag (S-CWs)) were established to evaluate nutrients and a typical MCs variant (i.e., MC-LR) removal efficiency from eutrophic water affected by the presence of plant and different substrate. The response of the microbial community to the above factors was also analyzed in this study. The results indicate that the presence of plant can generally enhance nutrients and MC-LR removal efficiency in CWs, except for I-CWs. Throughout the experiment, all CWs exhibited good nitrogen removal efficiency with removal percentages exceeding 90%; TP and MC-LR average removal efficiency of C-CWs and I-CWs were greater than G-CWs and S-CWs irrespective of the presence of plant. The best MC-LR removal efficiency under different MC-LR loads was observed in planted C-CWs (ranged from 91.56% to 95.16%). Except for I-CWs, the presence of plant can enhance relative abundances of functional microorganisms involved in nutrients removal (e.g., Comamonadaceae and Planctomycetaceae) and MCs degradation (e.g., Burkholderiaceae). The microbial community diversity of I-CWs was simplified, while the relative abundance of Proteobacteria was highest in this study. The highest relative abundances of Comamonadaceae, Planctomycetaceae and Burkholderiaceae were observed in planted C-CWs. Overall, ceramisite and iron-carbon were more suitable to be applied in CWs for nutrients and MC-LR removal. This study provides a theoretical basis for practical application of CWs in eutrophication and MCs pollution control. (C) 2020 Elsevier Ltd. All rights reserved.