Metal-polluted areas, especially where municipal sewage is used as fertilizer, often have high concentrations of more than one metal. The development of the root system is regulated by a complex signaling network, which includes reactive oxygen and nitrogen species. The delicate balance of the endogenous signal system can be affected by various environmental stimuli including heavy metals (HMs) in excess. Our goal was to analyze the microelement homeostasis, root architecture, and to determine the underlying changes in the nitro-oxidative status in the root system of rapeseed (Brassica napus L.) and sunflower (Helianthus annuus L.) subjected to combined HM treatments. The effect of model-sewage in two different layouts was simulated in rhizotron system by only supplementing the highest HM concentrations (Cd, Cr, Cu, Hg, Ni, Pb, and Zn) legally allowed. The two species reacted differently to combined HM treatment; compared to the relatively sensitive sunflower, rapeseed showed better metal translocation capability and root growth even at the more severe treatment, where the pattern of protein tyrosine nitration was reorganized. The obtained results, especially the increased nitric oxide content and changed pattern of tyrosine nitration in rapeseed, can indicate acclimation and species-specific nitro-oxidative responses to combined HM stress.