The causes of roof damage found on a large-scale water storage tank were investigated using hydrodynamic analysis. All operation and weather data, such as temperature inside and outside of the storage tank, atmospheric pressure, water level according to time, condensed water check inside pipelines, snowfall, and wind speed, were precisely reviewed. Four potential scenarios were postulated to estimate the vacuum pressure, presumed to be a direct cause of the roof damage to the storage tank. In the scenarios, an energy equation with a friction loss for pipelines and fittings was adopted to compute the pressure differences between the inlet and outlet of the ventilation and overflow pipes. A timewise pressure drop for the condition of fully clogged connected lines during a discharge operation was also carried out. A sequence solution for the unsteady Bernoulli equation to represent the dynamic motion of a water column inside a loop seal was successfully derived. This can predict the vacuum pressure limit inside the storage tank required to drain out the water from the loop seal. The predicted vacuum pressure was compared with the vacuum pressure required to cause the buckling phenomena at the roof support structures. In-depth analysis of each scenario showed that the roof damage of the storage tank developed when the vacuum pressure reached over the estimated vacuum pressure limit. To prevent further roof damage, including the storage tank of the same design at other plant, change of the layout of the air ventilation line was recommended.