The objective of this work was to compare and simulate transport and fate of microorganisms from wastewater for surface and subsurface irrigation methods. Adsorption isotherms and water-content dependent survival were measured for fecal coliforms, somatic coliphages and F-specific RNA phages in batch experiments with treated wastewater and clay loam soil. Column experiments with surface and subsurface trickle irrigation were carried out for the same soil. Results of the column experiments were simulated with a combination of Richards equation for water transport and advective-dispersive model with the first-order nonlinear adsorption and moisture-dependent first-order die-off. Simulations showed that die-off rates in column experiments were much higher than in batch experiments for all three organisms. Somatic coliphages were the most persistent organisms probably because of lower adsorption and die-off. The subsurface irrigation appeared to be efficient in decreasing the number of pathogens in irrigated water and preventing their appearance on soil surface that could lead to produce contamination.