Bacterial, viral and parasitic pathogens in swine wastes are of public health concern because many are able to infect humans. Hence, treatment processes must be effective in removing or destroying these microbes before wastewater discharge. Primary treatment by anaerobic lagoon is the current best management practice (BMP) for swine wastewater in the USA but alternative processes were also investigated for their potential to improve treatment. Wastewater samples were collected approximately monthly from March-December 1997 at a North Carolina swine nursery. Geometric mean concentrations for bacterial indicators (faecal coliforms, E coli, enterococci and C perfringens spores) in lagoon effluent were 3.3×105, 2.8×105, 3.4×105 and 2.2×104 CFU/100mL respectively. For somatic and male-specific coliphages they were 1.4×105 and 5.0×103 PFU/100mL respectively. Bacterial indicator levels in swine lagoon effluents are much higher than allowed for municipal wastewater effluents discharged to land or water. The anaerobic lagoon achieved reductions of 1.1–2.2 log10 for all indicators except C perfringens spores (0.2 log10). Of the secondary treatment processes, constructed wetlands achieved the best indicator microbe reductions ranging from 1.1–2.5 log10. A media filter and an overland flow system achieved mean indicator reductions of only 0.2–1.2 and 0.2–0.8 log10, respectively. The results indicate that a primary-secondary treatment system, an anaerobic lagoon and constructed wetlands, can achieve reductions of 2.9–4.8 log10 for bacterial and viral indicators and 1.5 log10 for C perfringens spores.