Contaminant intrusion in pipelines during transients is a remarkable mechanism, which leads to a decline in the quality of the contained water. The negative pressure of water hammer pressure waves is the trigger for the suction of pollution from the surrounding leak area, and hence deteriorating water quality. The volume of contamination intruded into the pipeline is investigated using mathematical and numerical modeling of the phenomenon. To elucidate this phenomenon in real pipe systems, the intrusion amount is estimated for 72 different scenarios including: two lengths of pipeline (i.e. short and long), three different leak locations, three different fluid velocities in the pipe, two leak diameters and two pipeline materials (elastic and viscoelastic). The results showed that the amount of intrusion in viscoelastic pipes was clearly less than that in elastic pipes, especially in long pipelines. The critical zone of high intrusion risk is identified close to the downstream valve for small leak sizes, nevertheless, it is difficult to estimate this zone in the case of large leaks due to significant interactions between nodal components (valve, leak, reservoir).