Background: The Iraqi environment, especially in the southern region, has been contaminated as a result of human activities. The detection of heavy metals in water samples is the preferred method for monitoring the toxic levels, which are very important for environmental protection and human health. Methods: Heavy metal concentrations of lead (Pb), cadmium (Cd), and nickel (Ni) were investigated in water samples from Al-Muthanna governorate, southern Iraq. The selected water samples were taken from different sources of tap water and river samples from the Euphrates and collected from various locations: residential, agricultural, and industrial. Results: The mean values of Pb, Cd, and Ni in tap water samples are 3.76, 2.62, and 84.88 μg/L, respectively, while the corresponding element levels in river water are 11.21, 7.58, and 104.31 μg/L, respectively. Rivers water samples recorded higher levels of toxic metals than tap water samples. Concentrations of toxic elements in water samples from industrial locations of Al-Muthanna governorate are higher than in the agricultural and residential places. Toxic metals in water samples can be arranged in the following sequence: Ni > Pb > Cd. Conclusion: The levels of heavy metals in most water samples were above the permissible levels according to USEPA; therefore, it is recommended that the water samples should be regularly monitored for heavy metals to prevent the effect of heavy metals contamination in the human food chain.