Potentially toxic elements (PTEs) distribution and speciation follow up become one of the most challenging issues in the last decades owing to their hazardous health impact. The element's species determines its toxicity, mobility, bioavailability and treatment possibility. This study focuses on the distribution and speciation of PTEs in Qena Governorate Groundwater by using GIS, MINTEQ and chemical techniques. Twenty-eight samples were collected and chemically analyzed according to standard methods. The concentrations of Fe, Mn, As, Cd, Cr, Ni and Pb were 25.95, 12.25, 8.07, 1.92, 52.35, 19.52 and 7.2 µg/L, respectively. Geochemically, the aquifer environment is reducing as appeared from negative value of Oxidation-reduction potentiality. Water-rock interaction is prevailing in this area with forward ion exchange reactions. Based on WHO specifications for drinking water, the studied samples have acceptable concentrations of Fe and Ni, but some samples have undesirable levels of Mn, As, Cd, Cr and Pb. The speciation model indicated that the studied elements occur as (HAsO4)-2, Cd+2, Cr(OH)3, PbCO3, Ni+2, Fe(OH)2+. These species are mostly of low toxicity and aquifer chemical conditions favor the co-precipitation of elements with iron hydroxides. Even though, the water can be used safely for irrigation with respect to PTEs. The main problem facing the use of this water for irrigation is the salinity (EC > 2250 µS/cm), in 71% of the studied samples. Finally, understanding the PTEs speciation in water will help comprehending the mobility, bioavailability and health hazards.