Four pathogenic virus removal mechanisms were investigated in a full-scale membrane bioreactor (MBR; nominal pore size 0.04 μm): (i) attachment of virus to mixed liquor solids; (ii) virus retention by a just backwashed membrane; (iii) virus retention by the membrane cake layer; and (iv) inactivation. We quantified adenovirus, norovirus genogroup II (GII), and F+ coliphage in the influent wastewater, the solid and liquid fractions of the mixed liquor, return flow, and permeate using quantitative PCR (adenovirus and norovirus GII) and infectivity assays (F+ coliphage). Permeate samples were collected 4–5 days, 1 day, 3 h, and immediately after chlorine enhanced backwashes. The MBR achieved high log removals for adenovirus (3.9 to 5.5), norovirus GII (4.6 to 5.7), and F+ coliphage (5.4 to 7.1). The greatest contribution to total removal was provided by the backwashed membrane, followed by inactivation, the cake layer, and attachment to solids. Increases in turbidity and particle counts after backwashes indicated potential breakthrough of particles, but virus removal following backwashes was still high. This study demonstrates the ability of the MBR process to provide over 4 logs of removal for adenovirus and norovirus GII, even after a partial loss of the cake layer, and provides evidence for assigning virus disinfection credit to similar MBRs used to reclaim wastewater for reuse.