Aquifer thermal energy storage (ATES) is an underground thermal energy storage technology with a large potential to decarbonise the heating and cooling of buildings. ATES installations typically store thermal energy in aquifers that are also exploited for potable water, so a major consideration during development is ensuring that system operation will not lead to groundwater pollution. In this study, the risk of contamination due to upconing of a shallow freshwater/saltwater interface during ATES operation is investigated. Fluid flow, and heat and salt (chloride ion) transport are simulated in a homogeneous aquifer during ATES operation via a well doublet. The impact of geological, hydrological and operational parameters is investigated in a sensitivity analysis. Two new dimensionless numbers are proposed to characterise salt upconing and redistribution during ATES operation and provide a close match to simulated concentrations: CR,w characterises the contamination risk at the ATES installation, and CR,d characterises the risk at locations downstream of the ATES installation with respect to background groundwater flow. ATES systems with CR,w and CR,d < 10 introduce low risk of contamination in a homogenous aquifer, with chloride concentration at, and downstream of, the ATES system, remaining below the World Health Organisation’s advised limit. ATES installations with CR,w and CR,d > 10 cause a rapid increase in aquifer chloride concentration. The results are used to estimate an exclusion distance beyond which ATES system operation will not cause contamination in a homogenous aquifer. The dimensionless parameters proposed allow rapid assessment of the potential for saltwater contamination during ATES operation.