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In this paper we present a self-organizing emergent multi-agent system designed for the decentralized real time control of water distribution networks. The agents, which are associated with every pump, tank, and water tower of such a distribution network, interact by means of a decentralized coordination mechanism based on digital info chemicals. In particular, they utilize a biologically-inspired coordination strategy, called indirect defense, which is used by certain plants in nature in order to get rid of herbivores. The experiments, which we have conducted on several different water distribution networks including one real-world municipal distribution network, demonstrate that the presented variants of our approach are able to achieve a self-organizing emergent solution comparable to the decisions made by inexperienced as well as experienced human operators, but with a higher flexibility, robustness, scalability, adaptivity, and autonomy.