This paper considers the introduction of a contaminant into a water supply system using a backflow attack. The recent development of techniques for water network sectorization, aimed at improving the management of water systems, is also an efficient way to protect networks from intentional contamination and to reduce the risk of the dangerous effects of network contamination. Users can be significantly protected by isolated district meter areas (i-DMAs) in the water network and the closing of the gate valves by a remote control system to implement such i-DMAs in cases of malicious attacks. This study investigates the effects of different approaches for water network partitioning and sectorization to protect networks using a technique for designing i-DMAs that is compatible with hydraulic performance and that is based on graph theory and heuristic optimization. For this analysis, the introduction of cyanide through a backflow attack was assumed. The methodology was tested on a large water network in Mexico and displayed good protection from a malicious attack.