Algal cell proliferation has posed significant problems for traditional water treatment facilities; these problems are attributed to surface hydrophilicity and electrostatic repulsion. Biological aerated filters (BAFs) have been extensively used in wastewater treatment to remove pollutants such as algal cells by utilizing the adsorption and separation capabilities of the filter media. In this study, a BAF was supplemented with biological filter medium (Marchantia polymorpha) to assess its effectiveness of pretreating aquaculture wastewater. In terms of process performance, steady and consistent treatment was achieved by the BAF withM. polymorpha(BAF2) under an algal cell density as high as 1.65 × 108cell/L, with average removal rates for NH4+-N and algae cells of 74.4% and 81.9%, respectively. The photosynthetic activity parameters (rETRmax, α, Fv/Fm, andIk) of the influent and effluent were quantitatively assessed, andM. polymorphawas found to remove algae by disrupting the photosynthetic system of the algal cells. Furthermore, the addition of theM. polymorphafilter medium enhanced the community structure of the functional microbes in the BAF system. The highest microbial community richness and diversity were observed in the BAF2. Meanwhile,M. polymorphapromoted an increase in the abundance of denitrifying bacteria, includingBdellovibrioandPseudomonas. Overall, this work offers a unique perspective on the aquaculture wastewater pretreatment process and BAF design.