Ophiolitic formations play a critical role in the groundwater resource of numerous countries and areas. Previous studies show that the structural heterogeneities of these rocks, coming from the presence of both different lithological units and multi-scale discontinuities, result in complex hydrogeological features that are not well characterized yet. In particular, there is a need for understanding how these heterogeneities impact the hydrodynamic properties of ophiolitic aquifers and the highly variable chemical composition of the water. To this end, we conduct various kinds of pumping experiments between two boreholes 15 m apart in the ophiolitic formation of the Batin (BA1) site in the wadi Tayin massif of the Sultanate of Oman. Cross-borehole open pumping experiments, as well as multi-level pumping and monitoring hydraulic tests, are performed in conductive zones that were identified from temperature and flowmeter data, but also in low-permeability zones requiring to manage very low pumping flow rates. The collected data are interpreted with a model implementing non-integral flow dimension, leakage and time-dependent pumping flow rates. The considered modeling concepts and the estimated hydrogeological properties show that the multi-directional structural heterogeneities of ophiolitic aquifers are key features that must be considered in future hydrogeological models because they drive the hydraulic responses of these systems.