There is an increasing overdependence and use of atrazine herbicide for the control of pre-and post-emergence broad leaf weeds on maize farms in rural agricultural communities in Nigeria. We carried out a survey of atrazine residue in 69 hand-dug wells (HDW), 40 boreholes (BH) and 4 streams from all the 6 communities (Awa, Mamu, Ijebu-Igbo, Ago-Iwoye, Oru and Ilaporu) in Ijebu North Local Government Area, Southwest Nigeria. The effect of the highest concentration of atrazine detected in the water from each of the communities on the hypothalamic-pituitary-adrenal (HPA) axis of albino rats was investigated. Varying concentrations of atrazine were detected in the HDW, BH and stream waters sampled. The highest concentration of atrazine recorded in the water from the communities ranged from 0.01 to 0.08 mg/L. Although there were no significant differences (p > 0.05) in serum levels of corticosterone, aldosterone and ROS of rats exposed to 0.01, 0.03 and 0.04 mg/L concentrations of atrazine compared to control, a significant increase (p < 0.05) was observed at 0.08 mg/L. Catalase activity increased significantly (p < 0.05) only at 0.03 and 0.04 mg/L of atrazine exposure. Butyrylcholinesterase activity, lipid peroxidation and serum ACTH of rats exposed to all the atrazine concentrations were not significantly different (p > 0.05) compared to control. Atrazine at environmentally relevant concentrations of 0.01, 0.03 and 0.04 mg/L detected in the water may not affect the HPA axis, attention should be given to 0.08 mg/L, which increases the serum corticosterone and aldosterone of the exposed rats.