Release of manure-borne Cryptosporidium parvum oocysts is the most probable cause of ground and surface water contamination with this pathogen. Our objective was to assess the effect of water saturation on transport of manure-borne oocyst through soil cores. Manure seeded with oocysts was applied on the surface of 10 cm columns filled with either sandy loam or clay loam soils. An eight-hour rainfall simulation provided saturated flow in one set of columns whereas the other set had suction ca. 5 kPa applied at the bottom. The convective-dispersion model with exponential release boundary condition, instantaneous adsorption and first-order kinetic removal of oocysts was used to simulate the transport. Transport parameters were found by fitting the van Genuchten analytical solution to the oocyst profile distributions. Oocysts stayed mostly within the top 8 cm of soil columns. Cumulative oocyst contents in leachates from unsaturated columns were less than 0.1% whereas the saturated columns allowed breakthrough of 0.4 and 1.3% in sandy loam and clay loam soil cores, respectively. The model mimicked the profile distributions of oocysts very well, but failed to simulate breakthrough of small amounts of oocysts. Values of retardation coefficient were less than unity in saturated columns and greater than unity in unsaturated columns. Values of the soil partition coefficient Kd derived from the retardation coefficient values were much less than values reported earlier from batch experiments with the same soils. The removal rates were much higher in saturated than in unsaturated columns. Soil water saturation substantially affected the manure-borne oocyst transport.