Hydropower plant vibrations due to pressure fluctuations and their troubleshooting methods are some of the most challenging issues in power plant operation and maintenance. This paper targets these fluctuations in a prototype turbine in two geometries: the initially approved design and the as-built design. Due to topographic conditions downstream, these geometries slightly differ in the draft tube height; the potential effect of such a slight geometrical change on the applicability of troubleshooting techniques is investigated. Therefore, the water flow was simulated using the CFD scheme at three operating points based on the SST k–ω turbulence model, while the injection of water/air was examined to decrease the pressure fluctuations in the draft tube, and the outputs were compared with no-injection simulations. The results show that a slight change in draft tube geometry causes the pressure fluctuations to increase 1.2 to 2.8 times after 4 s injecting at different operating points. The modification in the location of the air injection also could not reduce the increase in pressure fluctuations and caused a 3.6-fold increase in pressure fluctuations. Therefore, the results show that despite water/air injection being a common technique in the hydropower industry to reduce pressure fluctuations, it is effective only in the initially approved design geometry. At the same time, it has a reverse effect on the as-built geometry and increases the pressure fluctuations. This research highlights the importance of binding the construction phase with the design and troubleshooting stages and how slight changes in construction can affect operational issues.