Dissolved manganese (Mn (II)) can cause discoloration in water, laundry, and household surfaces, and cause operational problems in water distribution when it is oxidized. Because of these mostly aesthetic problems, the United States Environmental Protection Agency (USEPA) has set a secondary maximum contaminant level (SMCL) of 0.05 mg/L for manganese (EPA, 2023). Common removal methods for Mn (II) include oxidation followed by particle separation and adsorption with catalytic oxidation by filter media. These methods include the use of strong oxidants, often chlorine, which can generate carcinogenic disinfection byproducts (DBPs). Biological filtration of Mn is a treatment process which utilizes microbial activity to remove Mn. Biological filtration of Mn can have lower operational and maintenance costs while also avoiding using oxidants that could form harmful DBPs. The mechanisms by which Mn is removed in biologically active filters are not yet well understood. Different groups of Mn-oxidizing organisms employ different mechanistic pathways of oxidizing dissolved Mn (largely Mn(II)) leading to formation of particulate Mn oxides. The resulting biologically formed Mn oxides in biofilters can potentially further catalyze abiotic adsorption and oxidation of dissolved Mn. Many studies have demonstrated that the removal of Mn in typical drinking water treatment is a combination of biotic and abiotic mechanisms. This dissertation is focused on refining the definitions of biotic and abiotic mechanisms of overall Mn removal in biofiltration by characterizing microbial and chemical byproducts of Mn biofiltration. Chapter 1 of this dissertation introduces the problem statement, background literature, and hypotheses to be examined in following chapters. Chapter 2 provides information for operational parameters, biogenic oxide and media surface characteristics, and taxonomic profiles for full-scale Mn biofilters in New England. Chapter 3 explores how different parameters such as pH, dissolved oxygen (DO), media type, and culture type affect Mn uptake in batch mode reactors. Chapter 4 focuses on testing different media types, including ceramic and sand media, Mn oxide coated media, nutrient amendment, and mixed versus. Pure culture seeding can affect the acclimation of lab-scale column-based biotic Mn media filters. Chapter 5 provides a general summary of the findings in this dissertation and discusses future work.