Pathogen intrusion is a phenomenon that can cause a serious pollution problem in drinking systems. The paper describes the entry of external fluids through pipe defects caused by a pressure drop. This situation is especially important during hydraulic pressure variations. Pressure variations that can cause intrusion are analyzed in this paper. Three cases of pressure transients are modeled with the leak located near the transient origin, thus creating a critical scenario to force the intrusion. A combination of the method of characteristics and computational fluid dynamics is implemented in order to quantify the intrusion and leakage volume during the transient event in a pipe. Laboratory procedures provided data for validation of the results. The objective of this paper is to obtain the volume of intrusion and leakage during the pressure variations through defects in pipes. The flow resulting from the intrusion event will be quantified during the transient pressure, noting the potential implications of this event for public health.