Groundwater samples contaminated with potentially toxic elements (PTE), including metals and nitrate ions, were collected at a depth of 8–10 m from the Siberian Chemical Plant multicomponent waste storage. The possibility of developing a permeable biogeochemical barrier with zeolite and lightweight expanded clay aggregate (LECA) was investigated. The mass fraction and properties of several metals (Mn, Fe, Co, Ni, Cu, Zn, Cd, Hg and Pb) were determined to investigate their fixation on the chosen materials at the given experimental conditions. It was established that metals in sulfide or phosphate forms can be effectively immobilized via biomineralization on LECA, whereas metals from the non-chalcogen group are primarily retained in the form of phosphates. The formation of biogenic deposits of iron sulfide, which serve as a sorption–precipitation phase during the immobilization of the majority of metals, is an important aspect of the LECA loading process. The use of LECA and zeolite in the form of a two-component barrier is feasible based on the data obtained. It is assumed that metal immobilization processes occur due to sorption mechanisms in the zone of zeolite loading. Microbial nitrate removal and the formation of iron sulfide phases under reducing conditions, which form a geochemical barrier for metals, are expected in the LECA zone.