This study aims to estimate the migration and accumulation of metals (Cu, Zn, Fe, Mn, Ni, Pb, Cd, Co, Cr, Zr, Ba, and Sc) in terrestrial and aquatic landscapes. The research is based on the results of a long-term study (1998–2018) in one of the copper mining centers in Russia in the vicinity of Sibay City in the Southern Urals. The metal contents in samples of water, bottom sediments, soils, plant shoots (total aboveground phytomass samples, agrobotanical group samples, and shoots of indicator terrestrial and aquatic species), and fish muscles are measured. It is found that within natural geochemical anomalies, the migration ability of chemical elements in the soil–plant system and general biogeochemical cycle is low because of the high soil buffer capacity (determined by the high humus content, high percentage of fine fractions in granulometric composition, and neutral pH) and the adaptation of local plants to ore mineralization. The ecosystems affected by low pollution maintain natural homeostasis, stabilize the flow of chemical elements, and preserve the natural features of geographic components. Metal pollution and the replacement of natural steppe vegetation with secondary herbaceous-ruderal communities in critical areas near copper–zinc mining objects can stimulate the mobilization and inclusion of chemical elements in biogeochemical cycling, as well as the disruption of bonds among landscape components. The water systems in catenae function as stabilizers through a system of geochemical barriers and low uptake of metals by hydrophytes, such as the common reed (Phragmites australis).