Samples collected from two swine manure treatment systems including: swine manure treatment system and demonstrative unit (SMTS and DU), were analyzed by qPCR to quantify the amount of porcine adenovirus (PAdV) and porcine circovirus (PCV2) present. Positive samples were tested for virus integrity using DNase assay. Fifty-six water samples were collected monthly from March 2009 to May 2010. PAdV genome was found 66% of the samples in the SMTS and in 78% of the samples in the DU system. PCV2 was detected in 96% of samples collected from the SMTS system and in 86% of samples from DU. DNase assay revealed that there were undamaged virus particles of both PAdV and PCV2 in all sampling sites in the SMTS. However, undamaged particles of both viruses were detected in samples from the DU system in the affluent and middle sites, though undamaged PCV2 was absent in the effluent samples.