Pathogen intrusion may occur in water pipes when negative pressures allow external flows to enter through failures or leaks and then mix with safe water. Based on the Fixed and Variable Area Discharge (FAVAD) theory and the orifice equations, an analysis is proposed to estimate the intrusion flow across defects in pipes considering different types of failure. The equivalent diameter of different round hole failures was considered in order to obtain the dimensions of the split failures that presented the same pressure drop. In addition, experimental scenarios were made with external porous media to model the intrusion flow in buried pipes. An inverse method for the orifice equation is proposed to obtain the intrusion flows generated by the variations of two section failures produced by the pressure drop inside the pipe. The orifice equation properly represents the intrusion flow by adjusting the discharge coefficient. Furthermore, the considerable variations in the failures area with negative pressures should be taken into consideration in the expressions that estimate the intrusion flow.