Irrigation water distribution systems are used to supply water to produce crops, but the system may also provide a protected environment for the growth of human pathogens present in irrigation water. In this study, the effects of drip tape installation depth and sanitization on the microbial quality of irrigation groundwater were evaluated. Drip tape lines were installed on the soil surface or 5 or 10 cm below the soil surface. Water samples were collected from the irrigation source and the end of each drip line every 2 weeks over an 11-week period, and the levels of Escherichia coli, total coliforms, aerobic mesophilic bacteria, and enterococci were quantified. Half of the lines installed at each depth were flushed with sodium hypochlorite for 1 h during week 6 to achieve a residual of 10 ppm at the end of the line. There was a statistically significant (P = 0.01) effect of drip tape installation depth and sanitizer application on the recovery of E. coli, with increased levels measured at the 5-cm depth and in nonsanitized lines, although the levels were at the limit of detection, potentially confounding the results. There was no significant effect of drip tape depth on total coliforms, aerobic mesophiles, or enterococci. In contrast, a statistically significant increase (P < 0.01) in the recovery of total coliforms was recorded from the ends of lines that received chlorine. This may be indicative of shedding of cells owing to degradation of biofilms that formed on the inner walls of the lines. These findings emphasize the need to better understand conditions that may lead to corrosion and increases in bacterial loads inside drip lines during flushing. Recommendations to growers should suggest collecting groundwater samples for testing at the end of drip lines rather than at the source. Guidelines on flushing drip lines with chlorine may need to include water pH monitoring, a parameter that influences the corrosive properties of chlorine.