There are many large scale pumping stations in Egypt operating under different conditions and serving irrigation and drainage operation. These pumping stations are subjected to mechanical and hydraulic problems generating dynamic loads, vibrations, and stresses affecting the structure. Safe working of these stations verifies the operation function and efficient water management and distribution. Failure and damage occur for these pumping stations lead to maintenance problems, environmental problems, and water management problems, or they can lead to rising of the water levels which may cause failure to the embankment of the canals and drains. This research was performed to estimate the effect vibrations of typical axial pumping station exposed to motor vibration. This effect should be considered in the design process or in the assessment of such structures. Dynamic tests were done using the ambient vibration technique during the operation of the motors. Eight accelerometers were used to measure the vibrations of the building. Finite element numerical model was developed for the building. Three concrete core specimens were taken from the structural elements of the building and exposed to compression tests to adjust the properties of concrete in the FE model. The natural frequencies were evaluated using the power spectra method for the measured data, and modal analysis for the numerical model. The numerical model was subjected to the real recorded signals (displacement response). The increase in the stress due to the vibrations was calculated and compared to the designed stress capacity of the structure specified by the Egyptian code for loads. Also, the upper limits of vibrations of the building were compared to the available standards. The analysis of the collected data, the experimental results, and the results of the numerical analysis are presented.