Abstract Background Reuse of treated wastewater is a long-standing yet increasingly vital approach to alleviating water scarcity challenges in agricultural development. To evaluate the impact of urban wastewater on changes in heavy metals and essential elements in apple (Malus domestica Borkh.) leaves, fruits, and soils, a two-year field experiment (2021–2023) was conducted on six-year-old ‘Golden Delicious’ apple trees grafted onto three rootstocks—MM111, MM106, and EM9. The experiment assessed the effects of various irrigation treatments, including 50% and 100% treated wastewater, well water (control), and well water with NPK and micronutrient fertilization. Results The application of fertilizer with well water significantly increased soil magnesium content in the EM9 rootstock. The highest foliar absorption and accumulation of nickel (Ni), lead (Pb), sodium (Na), and potassium (K) occurred in EM9; barium (Ba), boron (B), iron (Fe), zinc (Zn), and strontium (Sr) accumulated most in MM111; while calcium (Ca) and manganese (Mn) showed the highest levels in MM106. Conclusion EM9 was introduced as the best rootstock for limiting soil As, Co and Ba. MM111 limited the concentration of Ni in leaf but raised this elemt in soil. Under the critical water shortage conditions of the experimental site, irrigation with diluted treated wastewater either by mixing with well water or alternating with freshwater can serve as a sustainable and environmentally sound alternative to conventional irrigation. Keywords Arsenic, Barium, Calcium, Magnesium, Manganese

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