The Neelum–Jhelum Hydropower Project, commissioned in April 2018 and located in the Azad Kashmir region of northeast Pakistan, is one of the most challenging and technically complex projects in the region. The project’s 28.6 km headrace tunnels are constructed in a highly mountainous region with relatively complex geology that includes various sedimentary rocks of Murree formation. The hydro-mechanical behavior of the deep headrace tunnels with a maximum overburden of 2000 m and underground powerhouse at a depth of 450 m are of particular interest. The project generates electricity by diverting water from the Neelum River to an underground powerhouse through a tunnel system crossing beneath the Jhelum River. The pressurization of the hydraulic tunnels was an important milestone and necessitated intentional planning down to the smallest detail for the first filling. Successful filling was a governing criterion for proper functioning of the tunnel lining that was supplemented by monitoring instruments, a drainage system, and ground treatments during construction of the project. Ground re-saturation during the first filling of the concrete and shotcrete-lined waterways constructed in the diversified rock mass is interesting to study. The rock mass in this area is sheared and fractured, with open fissures. In this study, we investigated the ground re-saturation and water leakages in adits, plugs, and surface outflow after the first filling of the headrace tunnel. A load rejection test was conducted to evaluate overall fitness of the power waterways, plant, and to study any change in leakages due to sudden oscillation in the waterway tunnels. Surfer3D software was used to analyze the data collected from the piezometers, which showed abnormal water pressure built up in a localized zone between penstocks three and four. This study was also supported with two-dimensional finite element modeling of the project, at a location where the tunnel has minimum rock cover susceptible to hydrojacking. Numerical analysis results were compared with field data results during the first filling process and both showed close proximity.