Through nutrient recovery by urine separation, the VUNA project aims to develop an effective sanitation system that simultaneously helps address important issues such as environmental pollution and water scarcity. Refinement of the nutrient recovery process presents several challenges: at a technical level, as nitrifying bacteria are sensitive to several parameters; and from a public health perspective, as nutrient recovery from urine implies exposure to pathogens. As part of this problematic, the present study focused on four main objectives: operating nitrification reactors, characterising both virus and bacteria inactivation, and evaluating different inactivation mechanisms. Indicator organisms (bacteriophages and bacteria) were used as surrogates for human pathogens. In a first set of experiments, the bacteriophage MS2 was spiked continuously over 60 days in a continuous flow nitrification reactor. Nitrification did not affect the bacteriophage concentration within the reactor. The second set of experiments consisted of the operation of small scale batch and semi-batch reactors to test in total three different bacteriophages (X147, MS2, Qbeta) and two bacteria (Salmonella typhimerium, Enterococcus spp.) under varying parameters. Pathogens can be inactivated or affected by different mechanisms. Four possible inactivation mechanisms were further evaluated: 1) effect of biological activity in a nitrification treatment system, 2) effect of the air-water interface in a buffer (PBS) and nitrified urine, 3) effect of the complexity of solution, 4) effect of ambient temperature. Results indicated that nitrification caused bacterial inactivation but did not influence the bacteriophages concentration. Air-water interface did not affect bacteria and showed mixed results for bacteriophages. Ambient temperature was not an inactivating parameter for neither of the groups studied. Finally, the bacteriophages presented signs of resistance, possibly due to a protective effect of the complex solution in the nitrification reactor.