The specific surface area and topology of a biofilter media carrier is one of the most important parameters that determines the performance and efficiency of the system. In this work, mathematical models and 3D printing technologies were used to design and fabricate complex media designs that provide high specific surface area and refugia to protect biofilm from premature sloughing. Several gyroid based designs were proposed with specific surface area well beyond 2300 m2/m3. However, wall thicknesses and pore sizes that are prone to clogging determined a design that yields 1168 m2/m3 (133% larger than the baseline commercial K1 Kaldnes). Several moving bed bioreactors were constructed for laboratory testing with inoculation provided by wastewater from a fisheries operation. Preliminary results indicate that the 3D printed media can withstand the prevalent conditions in moving bed bioreactors, and that the NH3 removal rate of gyroid media is comparable to that of K1 Kaldnes. This work establishes the feasibility of using 3D printing for bioreactor media fabrication and allows for future topology optimization for enhanced operation. Future work is needed to investigate how these complex media designs might stimulate novel microbial assemblages and community metabolism that translate into yield efficiency gains in reactor performance.