Environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) are used to survey biodiversity non-invasively to mitigate difficulties in obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA were used to monitor known wildlife pathogens; however, most wildlife pathogens are unknown and often evolutionarily divergent. To detect and identify known and novel mammalian viruses from eDNA/iDNA, we used a curated set of RNA oligonucleotides as viral baits in a hybridization capture system coupled with high-throughput sequencing. We detected multiple known and novel mammalian RNA and DNA viruses from multiple viral families from both waterhole eDNA and leech-derived iDNA. Congruence was found between detected hosts and viruses identified in leeches and waterholes. Our results demonstrate that eDNA/iDNA samples represent an effective non-invasive resource for studying wildlife viral diversity and for detecting novel potentially zoonotic viruses prior to their emergence.