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When hot water is injected into an aquifer, the water will react with the minerals present in the aquifer. The most important processes are cation exchange, precipitation/dissolution of carbonates, and dissolution/precipitation of silicates. If the redox condition of the water is changed during the process (e.g., because of contact with oxygen in the air or because of mixing of water with a different redox status) redox reactions will be important as well. In many cases, the water will have to be treated to prevent carbonate scaling during heating. This treatment will influence the reactions in the aquifer. Because the water is (at least partly) reused each cycle, the reactions in the aquifer may cause an increase or a decrease in necessary treatment in subsequent cycles. Also, the treatment and the reactions in the aquifer may have an influence on the environmental impact of the store because the quality of the water lost from the store is changed.

In aquifer thermal energy storage (ATES) systems, wells provide the interface between the energy storage and use. Efficient operational wells are, therefore, essential for the system to run at maximum (design) efficiency. Adequate test drilling to accurately predict aquifer properties is essential in the design phase; proper construction and development are crucial; and proper monitoring of performance is necessary to identify the early stages of clogging and to evaluate the adequacy of well rehabilitation.