Polyacrylamide (PAM) use in irrigation for erosion control has increased water infiltration and reduced soil erosion. This has improved runoff water quality via lower concentrations of nitrogen, phosphorous, and pesticides, and decreased biological oxygen demand. Since non-toxic high molecular weight anionic PAMs removed clay size sediment particles in flowing water, it was hypothesized that PAM would effectively remove or immobilize microorganisms in flowing water. In an agricultural field at the USDA Agricultural Research Service, Idaho, USA, the efficacy of PAM-treatment of furrow irrigation water to remove several categories of microorganisms in the inflow and runoff was determined. Treatments were: (1) PAM application and a control; (2) three flow rates; (3) two distances from the inflow point; and (4) three times during each irrigation. After water travelled 1 m at 7.5 and 15.5/min, PAM-treatment reduced total bacterial and microbial biomass and total fungal biomass relative to the control treatment. After water travelled 40 m at 7.5, 15.5, and 22.5/min, PAM-treatment reduced algae, the numbers active and total bacteria, active and total fungal length, and total bacterial biomass, total fungal and microbial biomass relative to the control treatment. Although specific organisms were not identified or monitored in this study, the results clearly have implications for controlling the spread of soil-borne plant pathogens and other classes of harmful organisms within and among fields via irrigation water and in re-utilized return flows. Beyond furrow-irrigated agriculture, new methods to manage overland transmission of harmful microorganisms could potentially help control transport of pathogens from animal waste in runoff and groundwater.