The pipe system roles as a main bridge between membrane modules and pumps in membrane water treatment plants. Membrane operation modes generally consist of filtration and backwash processes in a normal mode, a pressure decay test as an integrity test and a chemical circulation through pipe system in a cleaning mode. Thus factors effecting on membrane performance should be sufficiently considered before design and operation. This study evaluated flow analysis for vibration diagnostic and evaluation of the fatigue lifetime in the microfiltration system applied for a drinking water treatment plant. Vibration of main membrane pipelines was measured to identify the source of vibration. Also natural frequency and fluid dynamics was calculated by computational fluid dynamics. It showed that maximum magnitude frequencies were at 12 Hz and 22 Hz, respectively at water and air pipeline during filtration and backwash. Backwash process caused mainly vibration on the backwash water pipe. The calculated frequency from analysis of frequency response and CFD was in a good agreement with the measured frequency. Fatigue analysis showed that pipelines were getting little damage caused by vibration. Fatigue lifetime was predicted more than 15 years under the operation condition of daily filtration, and more than 27 years under the operation condition of a daily backwash mode, resulting in minor damage on the pipe lifetime.