Media filters are important in wastewater recycling schemes for pathogen removal. Filter selection depends on health targets and plant scale; however, there is a data gap concerning pathogen removal efficacy at full scale. This study compared the pathogen removal performance of two full-scale filtration technologies, including a small 17 ML/d pressurized media filtration (PMF) plant and a large 120 ML/d gravity filter in the form of dissolved air flotation filtration (DAFF). The preceding clarification processes were also assessed. Validation of protozoa and virus removal was estimated by dosing model organisms yeast (Saccharomyces cerevisiae) and MS2 bacteriophage to demonstrate removal potential. The DAFF process (coagulation, flotation and filtration) was most efficient at removing bacteriophage with a mean log10 removal value (LRV) of 2.90 (±0.64), compared with 0.98 (±0.37) achieved by coagulation, sedimentation and PMF. Yeast log10 removal though both systems were similar measuring 3.80 (±1.06) through DAFF and 4.57 (±0.14) through coagulation, sedimentation and PMF. The DAFF process showed greater variability in MS2 and yeast removal, which was attributed to filtration. Energy and chemical usage were also evaluated, revealing trade-offs between these factors, treatment scale and pathogen LRVs, offering practical insights into the technological and economic aspects of designing fit-for-purpose recycled water schemes.