Membrane distillation (MD) is a desalination technology with promising applications in treating brines generated by reverse osmosis. Theoretically, MD can achieve 100% rejection of non-volatile contaminants such as organic and inorganic solutes and pathogens because only the vapor phase permeates through the membrane. However, polymeric membranes are subject to a wide distribution of pore sizes that may result in pore flow or liquid flux through even a new membrane resulting in poor contaminant rejection. In pilot-scale MD systems, a larger membrane area increases the hydraulic pressure in the flow channel and the transmembrane hydraulic pressure difference, thus increasing the probability of pore flow of non-volatile contaminants through the membrane and providing enhanced resolution of contaminant detection. This work reports membrane rejection of organic and inorganic non-volatile solutes in a pilot-scale air-gap MD (AGMD) element and quantifies, for the first time, transport of non-volatile solutes through the membrane because of pore flow. Pathogen rejection in the pilot-scale MD system was also measured using enteric virus surrogates MS2 and PhiX174 as tracers. Organic and inorganic solutes and both viruses were detected in the distillate, suggesting the presence of pore flow. No difference between organic and inorganic solute rejection was observed, and both decreased (from 2.5-log10 to 1.5-log10) with an increase in air-gap vacuum (from 50 to 500 mbar). At 50 mbar and low evaporator inlet temperature (40 °C), virus rejection (2.4 -log10) was higher than organic and inorganic solute rejection (1.7-log10).