Wastewater for irrigation in low- and middle-income countries can recharge aquifers and potentially contaminate supply sources. The infiltration rate has increased 13-fold in Mexico's Mezquital Valley, the largest agricultural area wastewater-irrigated worldwide, thus we assume that wastewater had contaminated supply sources. Fecal indicator bacteria (FIB) counts were enumerated in household water of two wastewater-irrigated areas, Tula and Tlahuelilpan, and a groundwater irrigated area, Tecozautla. During 2016–2017, household water, wastewater, and groundwater were sampled, analyzing fecal coliforms, fecal enterococci, and Escherichia coli, following membrane filtration procedures, and confirming the presence of E. coli by polymerase chain reaction. Nearly 50% of household water contained fecal contamination of up to 4.62 × 104 CFU/100 mL. Significant differences between FIB counts in household water from Tula and Tecozautla were observed by Kruskal–Wallis and Dunnett tests. Household water samples from Tula contained highest FIB counts. Wastewater from Tula and Tlahuelilpan contained counts of six orders-of-magnitude of FIB. Counts were high when residual chlorine was <0.2 mg L−1 and underwater storage. This research serves as a baseline to observe improvement with a newly installed wastewater treatment plant. Safe irrigation wastewater reuse should be performed under strict surveillance, considering human safety a priority.