Hydraulic tunnels, integral components of hydropower plant (HPP) systems, traversing diverse rock masses, pose challenges for long-term operation. The study’s main goal was to investigate how hydraulic transients originating from the headrace tunnel transfer through the concrete lining and manifest in surrounding aquifer systems. In this experimental study at the water pressure tunnel of HPP Pirot (Serbia), a novel monitoring approach was employed. The internal piezometers with highly sensitive probes are distributed strategically along the tunnel in different geological environments. This approach involved monitoring of water pressure in the surrounding rock masses and observing the impact of hydraulic transients generated by HPP operation. A comprehensive analysis of monitoring data, incorporating ordinal and partial correlations and considering geological features, provides a profound understanding of groundwater dynamics, pressure transient phenomena, and hydrogeological characterization during HPP operation. The study highlights the complex and spatially diverse hydrogeological environment, emphasizing the varying reactivity of pore pressure during HPP operation, particularly concerning Water Mass Oscillations (WMO). Reactive piezometers near the surge tank demonstrate significant pressure variations, while those located further away display synchronous pressure changes with reduced amplitudes. Schematic hydrogeological models have been created based on the hydraulic impacts of HPPs in different geological environments along the tunnel route. The water pressure response enabled aquifer characterization of (1) a thin-layered, low-fissured aquifer closely related to the reservoir, with low influence on WMO transients; (2) a low-fissured, compartment aquifer or non-aquifer with minimal to no influence on WMO transients; (3) a well-structured karst aquifer system influenced by WMO transients; (4) a fault-controlled zone of deep hypogene karst aquifer discharge highly influenced by WMO transients; and (5) an aquifer with a dominant development of the karst conduit system highly influenced by WMO transients. The study highlights the significance of monitoring water pressure within the rock mass as a fundamental element in analyzing the interaction between water pressure tunnels and the hydrogeological environment. Applying the presented instrumentation and methodology facilitates effective monitoring in research areas where pressure tunnels are constructed.