Drinking water distribution networks are critical infrastructures that are potential targets for terrorists’ attacks. Intentional contamination of the water distribution networks is the most serious of the possible attack scenarios. Although there has been many studies on how to protect the networks from the deliberate attack the knowledge about the decontamination of the systems is not sufficient to recover systems in reasonable time and put back into normal operation. This thesis focuses on the decontamination of the drinking water distribution system after the deliberate contamination with resistant microorganisms (spores of Bacillus anthracis) and pesticides (paraquat). In addition, processes occurring in the distribution systems were studied as well as their potential to interfere with the decontamination. Conventional treatments (shock chlorination, acid and alkaline flushing) and advanced oxidation processes were tested for the ability to inactivate Bacillus spores and degrade paraquat pesticide in batch scale and large scale pilot loop. Results showed that the quality of water influences the composition of loose deposits and vice versa. The distribution system sediments accumulate organic matter, but the concentration of the organic carbon in the deposits rather depends on the pipe material than the age. Large scale pilot study showed that shock chlorination is very effective against Bacillus spores in water; however additional treatments are necessary to inactivate the spores adsorbed to the surfaces. A novel approach of alternation of chlorine and the biofilm release agent (NaOH) showed the best results in inactivation of Bacillus spores on PVC pipe surfaces. Despite the diversity of the processes occurring in the distribution system it can not only interfere with the treatment processes but also the distribution system metal pipes benefit the heterogeneous Fenton reaction and increase the degradation rate of pesticides. The distribution system sediments may be used as catalysts for the reaction, however a special attention must be paid to the composition of the sediments.