Abstract Water quality index (WQI), pollution index (PI), and metal index (MI) were applied in the last reach of Diyala River, Baghdad, Iraq with regard to ten heavy metals (Cd, Cr, Cu, Ni, Pb, Mn, Fe, Zn, Ag, and Cn). These indices were applied to historical data along with the data obtained from the present study in order to acquire a historical heavy metal assessment of the river reach. The results of WQI showed that the water quality of the reach of interest declined from excellent in the year of 1999 to unsuitable in 2007 then good in 2008 to unsuitable once again in the years of 2009–2015. The PI indicated that Cd, Cr, and Pb were the most affecting elements all over the years. The MI was found to be a threshold of warning during all years but with different levels. The impact of Al-Rustimiyah Wastewater Treatment Plants (WWTPs) on the water quality was evident due to the lack of heavy metal treatment units within the plants. It is recommended to add such units to the WWTPs and to reduce the local electricity generators that contribute with great amounts of contaminants.