Microbial quality of irrigation water attracts substantial attention due to the increased incidence of gastrointestinal illness caused by contaminated produce. Little is known about the changes in microbial quality of water during its delivery to crops. Studies were conducted to compare the biofilm formation and changes in microbial water quality in aluminum and PVC irrigation pipes. Irrigation events were conducted weekly and sections of irrigation pipe (coupons) analyzed for total protein, for total and fecal coliform bacteria, and for Escherichia coli. Coliform and E. coil concentrations along with nitrate, orthophosphate, and total organic carbon were monitored in the intake surface water, output irrigation water, and measured in residual standing water in pipes just prior to each irrigation event. Proteins accumulated to a greater extent in aluminum-associated biofilms than in plastic-associated biofilms. Numbers of total coliforms associated with aluminum coupons increased with time while numbers of total coliforms associated with plastic coupons fluctuated. Nitrates disappeared in standing water after one week in aluminum pipes and remained present in plastic. No detectable E. coil remained in standing water in both types of pipe. There was a high probability that coliform concentrations in output irrigation water were different from the intake concentrations in plastic pipes but not in aluminum pipes. Further research is required to evaluate how pipe material may affect the potential of biofilms in irrigation distribution systems to serve as reservoirs of pathogens that can be disseminated to crops during irrigation. Published by Elsevier B.V.