The potential use of different hard and soft parts (otolith, scale, eye lens, dorsal spine, vertebral bone, muscle, and liver) of Rutilus kutum for biomonitoring of 13 major and trace elements (Br, Ca, Cl, Cu, Fe, K, Mg, Mn, Na, P, S, Sr, and Zn) was evaluated, for the first time. The specimens were sampled from three sampling sites in the Southern Caspian Sea in May 2016. Twenty specimens were collected from each site. The elements' concentrations in the samples were measured by proton-induced X-ray emission (PIXE). In all the hard tissues, except for eye lens, Ca was the most abundant element, whereas Fe was among the least abundant elements. The orders of element occurrence in the two soft tissues were largely similar. Ca, Fe, S, Cl, and K could be detected in all the selected tissues, while Br was detectable only in otolith. Minor similarities among the tissues were identified in the case of eye lens (concerning P, S, and Zn) and liver (in terms of Cl, Fe, and K), whereas, in the case of Sr and Ca, otolith shows the maximum distance. In general, it can be concluded that all the studied hard parts, except for eye lens, may offer alternatives for biomonitoring of Ca, Cl, Fe, K, and S in the southern Caspian Sea. The scales and spines represent a potential non-lethal alternative to the other hard parts.