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Nitrogen and fecal indicator bacteria (FIB) in runoff from concentrated animal feeding operations (CAFOs) can impair surface and groundwater quality. Bioretention systems are low impact nature-based technologies that can effectively treat CAFO runoff if modified with an internal water storage zone (IWSZ) or amended with biochar. In this study, the performances of four pilot-scale modified bioretention systems were compared to assess the impacts of (1) amending bioretention media with biochar and (2) planting the systems with Muhlenbergia. The system with both plants and biochar amendment had the best performance, with an average of 5.58 log reduction in E. coli and 98% removal of total nitrogen (TN). All systems treated the first pore volume well as new runoff flushed the treated water from the IWSZ. Biochar improved TN and FIB removal due to its high capacity to adsorb or retain ammonium (NH4+), dissolved organic nitrogen, dissolved organic carbon, and E. coli. Planting improved performance, possibly by increasing rhizosphere microbial activity.