Clusters of industrial plants often generate contaminant plumes with several potential sources. Prevention of further pollution and designing suitable remedial measures require identification of the contributing source among all potential ones and the sorting of currently active sources from historical ones. In the study area, an industrial complex in the Negev desert, Israel, contaminants could not serve as indicators for the contamination sources because of their extensive spatial distribution across the site. However, stable isotopes of oxygen, hydrogen and sulfur, as well as tritium, proved to be efficient tools for this task. The isotopic characterization of the potential end members provided the criteria for constraining a contaminating source when several alternative sources appeared viable. The isotopic fractionation of oxygen and hydrogen isotopes could be tied to the various disposal phases of the industrial wastewater. The three case studies presented here confirm the important role of isotopes as tracers in contaminated sites.