In the field of research for designing and preparing innovative nanostructured systems, these systems are able to reveal the presence of heavy metals in water samples, and can efficiently and selectively interact with them, allowing for future applications in the field of water remediation. We investigated the electronic and molecular structure, as well as the morphology, of silver nanoparticles stabilized by mixed biocompatible ligands (the amino acid L-cysteine and the organic molecule citrate) in the presence of cadmium and arsenic ions. The molecular, electronic, and local structure at the ligands/silver nanoparticles interface was probed by the complementary synchrotron radiation-induced techniques (SR-XPS, NEXAFS and XAS). The optical absorption (in the UV-Vis range) of the nanosystem was investigated in the presence of Cd(II) and As(III) and the observed behavior suggested a selective interaction with cadmium. In addition, the toxicological profile of the innovative nanosystem was assessed in vitro using a human epithelial cell line HEK293T. We analyzed the viability of the cells treated with silver nanoparticles, as well as the activation of antioxidant response.