Water-rock interactions are sorption-, dissolution-, precipitation-, and redox reactions at the interface between rock matrix and water. In aquifer thermal energy storage (ATES) systems, certain water-rock interactions can have undesired consequences, such as clogging of aquifer pores or contaminant release, and are therefore geochemical risks. Their prediction and prevention requires site-specific knowledge about water-rock interactions at specific operational conditions. This study investigates the reactivity of two pyrite-bearing siliciclastic rocks from the Hettangian and Lower Sinemurian stages of the Lower Jurassic. They are associated with the heat storage aquifer of the ATES system at the German parliament buildings in the city of Berlin, which is located in the south-eastern part of the Northeast German Basin. The study presents a workflow to (a) describe mineralogy and sorption reactions at the rock surface, (b) quantify the maximum of potentially critical (mineral-forming/contaminant) elements that can be released from the rocks, (c) determine their phase association and release mechanisms, and (d) identify the most important control parameters and process interactions during heat storage. The bulk mineralogy was identified by X-ray diffraction, X-ray fluorescence and scanning electron microscopy. Potentially critical mobile elements and easily soluble crystalline and amorphous solid phases, such as hydroxides and sulfides, were quantified with a specifically developed sequential extraction. This method allows the partition of mobile elements by association with specific rock fractions with the help of appropriate solvents. These fractions are (1) exchangeable (2) associated with acid-soluble phases (carbonates), (3) associated with reducible phases (oxides/hydroxides), and (4) associated with oxidizable phases (organic matter/sulfides). Heat storage, defined by temperatures of up to 90 °C and potential intrusion of oxygen into the aquifer, was investigated by steady-state leaching experiments with simplified synthetic groundwater (0.42 M NaCl solution) by varying the control parameters temperature (25, 50, 70, 90 °C), solute oxygen (oxic/anoxic) and leaching time (1, 2, 4, 7 days). The influence of different control parameters and process interactions was analyzed by numerical simulations and statistics, using experimental data for parameterization and validation. The following results and implications for ATES operation in the originally oxygen-depleted aquifer were found for the potentially critical (contaminant/mineral-forming) mobile elements Al, As, Ba, Ca, Cu, Fe, Mn, Ni, Pb, and Si: The total leachable quantity of each element, i.e. the leached sum over all sequential extraction steps, is very small in the aquifer sandstone (<0.1 mg/g), and significantly higher in the siltstone of the topset aquitard (up to ca. 4 mg/g for Ca). The iron system is the main risk factor. At oxic conditions, pyrite (FeS2) dissolves. If no suitable buffers are present, the solution is acidified, which facilitates the mobilization of several other elements. At anoxic conditions, the dissolution of iron hydroxides is the process mainly controlling element mobilization. Ferric iron re-precipitates readily, and is the main mineral-forming species in the investigated system. Calcium is predominantly adsorbed, and can be mobilized by pH reduction. In case the solute concentration decreases due to mineral precipitation, Ca can be desorbed quickly to regain thermodynamic equilibrium between rock matrix and groundwater. Small amounts of aluminum and silicon can be released rapidly from amorphous (hydr)oxides, which were their main source during leaching experiments of up to seven days. Kinetically slow dissolution of crystalline silicates prevails during longer leaching periods. Arsenic is nearly immobile in the aquifer sandstone. During the experiments, it was released only in the reduction step of the sequential extraction (ca. 0.02 µg/g), and represents no critical risk. Barium, copper, nickel, and lead have no single phase association. They are probably mainly present as solid solutions or co-precipitates, and their mobility seems to be primarily controlled by iron phase dissolution/precipitation. Copper was also found in elementary form. For the investigated heat storage at the German parliament buildings, these findings indicate no critical risk factors, which could lead to groundwater contamination or porosity reduction in dimensions that would prohibit ATES operation. However, constant nitrogen pressurization of the system is imperative to prevent oxygen intrusion, which could eventually lead to pyrite dissolution, groundwater acidification once its buffering capacity is exceeded, and critical element mobilization.