Ground source heat pump (GSHP) systems play a key role in the exploitation of shallow geothermal energy as a renewable energy source. In clay-sulfate rocks, however, rock swelling is a major threat to the success of GSHP projects that may require extensive and costly countermeasures to mitigate the effects. Swelling is in these cases triggered by water ingress into expansive anhydrite bearing rock layers, followed by the chemical transformation of the sulfate mineral anhydrite to gypsum upon contact with water. Thus, assessing, understanding and quantifying coupled hydraulic and geochemical changes in the swelling zone is essential for selecting effective countermeasures. The present study examines these processes for a study site in Staufen, Germany, where an improper borehole heat exchanger (BHE) installation has allowed ingress of water into the clay-sulfate bearing strata of the Gipskeuper, followed by swelling and substantial heave of the land surface. A reactive transport model was employed to isolate the key processes and to evaluate a range of mitigation scenarios. The model simulations allowed for the assessment of (i) water inflow into the swelling zone, (ii) water availability for the transformation of anhydrite into gypsum within the swelling zone, and (iii) the potential for future swelling for each of the considered scenarios. Our results indicate that even with incomplete BHE sealing, water flow into the swelling zone and thus the swelling process can be arrested through appropriate hydraulic countermeasures. In contrast, our worst case scenario simulation predicts a further 10 cm of heave at the ground surface by 2025. The results illustrate the importance of integrating geological, hydraulic and geochemical information when assessing and predicting the efficiency of site-specific mitigation measures.