Abstract Background The analysis of the negative effects of environmental metal pollution is complex and difficult to assess, because the great number of variables and levels of biological organization involved. Therefore, an integral interpretation of the structure of ecological interactions from the multifactorial toxicological vision can be achieved by the use of new analysis tools, such as the complex network theory analysis (CNT). Results Our results demonstrated that the trophic level has an effect on metal enrichment, being the detritivores who presented the highest bioaccumulation levels in comparison to plants, as well as higher biomagnification levels in the soil-plant-detritivores relationship. Also, Vachellia farnesiana displayed greater sensitivity to genotoxic damage than Eisenia fetida. Finally, the analysis of complex networks showed that detritivores are the key link in this dynamics, on which the interactions between heavy metals, plant and detritivores depend. Conclusions This study shows that there is an effect of the study site on heavy metal bioaccumulation and DNA damage induction, and that these responses are particular to each species and to each bioaccumulated metal, which in turn reveals specific sensitivity for each trophic level. Moreover, the application of CNT methodology allowed us to clarify in this particular system, the interaction types and the principal components of the trophic structure.