<p>Within the KONATES project, a pilot system was set up in the Science Park in Leipzig to investigate the feasibility of combining Aquifer Thermal Energy Storage (ATES) with groundwater remediation. Along with the circulation and storage of heat through groundwater, a novel zeolite adsorbent and stripping module were used to remove chlorinated hydrocarbons from the extracted groundwater. However, the operation of the ATES system posed challenges due to urban constraints, primarily related to temperature limits and complex infrastructure. To address these limitations, a 3D numerical model was developed to simulate hydraulic and heat transport processes. The model predicted that the ATES system could operate in 10-day active phases at <InlineEquation ID="IEq1"> <EquationSource Format="TEX">\(0.6\,\text{m}^3\)</EquationSource> <EquationSource Format="MATHML"><math> <mrow> <mn>0.6</mn> <mspace width="0.166667em" /> <msup> <mtext>m</mtext> <mn>3</mn> </msup> </mrow> </math></EquationSource> </InlineEquation>/h and <InlineEquation ID="IEq2"> <EquationSource Format="TEX">\(70\,^\circ\)</EquationSource> <EquationSource Format="MATHML"><math> <mrow> <mn>70</mn> <mmultiscripts> <mspace width="0.166667em" /> <mrow /> <mo>∘</mo> </mmultiscripts> </mrow> </math></EquationSource> </InlineEquation> injection temperatures with one day of storage time, resulting in a maximum <InlineEquation ID="IEq3"> <EquationSource Format="TEX">\(4\,^\circ\)</EquationSource> <EquationSource Format="MATHML"><math> <mrow> <mn>4</mn> <mmultiscripts> <mspace width="0.166667em" /> <mrow /> <mo>∘</mo> </mmultiscripts> </mrow> </math></EquationSource> </InlineEquation>C groundwater temperature increase at the boundary to the neighbouring properties. This work demonstrates the usability of 3D coupled hydrothermal models in designing ATES systems in a complex urban environment.</p>