Solid and liquid wastes from livestock operations represent important challenges for animal production regarding their impact in the environment and public health. Parasitological tests performed on 80 samples of affluent and effluent waters from three anaerobic biodigestors with flexible structure from swine farms of Caldas - Colombia, showed the presence of Isospora suis (45%), Eimeria suis (42.5%), E. espinosa (35%), Strongyloides ransomi (28.8%), E. perminuta (12.5%), E. cerdonis (3.8%), and E. porci (2.5%). The additional finding of eggs of Taenia spp. in 10% of the samples was probably caused by a connection between the human sewage system and the biodigester. Although we observed a mean decrease of 65.6% of parasites, these levels were insufficient to meet the minimum requirement set by Engelberg's guidelines regarding water quality. This study demonstrates the serious environmental impact that an inadequately treated animal wastewater represents, and has important implications for water resources and human health.