In this study, the levels of metallic elements (Al, Cr, Cu, Fe, Mn, Ni, Pb, Sc, V, and Zn) and radioactive tracers (excess 210Pb and 137Cs) were determined in three sediment cores using Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES) and gamma spectrometry, respectively. These samples were collected from the Santos-São Vicente Estuarine System (SSVES) on the western South Atlantic coast. This work, involving multivariate statistics and time-series analysis, discussed how anthropogenic pressures and climate-related processes impact the metal content in sediments deposited in this heavily industrialized coastal system. The sedimentation rate increased during the late 1960s, particularly during the 1970s and 1980s, corresponding to the period of heavy investments in industrial and urban development of the SSVES over the last seven decades. Principal component analysis generated two factors that explained between 57% and 87% of the variance in the elemental content of the sediments in each core. The first component, referred to as the natural component, showed a decreasing trend after 1970. Meanwhile, the second component, the anthropogenic component, correlated with Cu, Pb, and Zn, and increased during the same period. Time-series REDFIT analysis demonstrated that the natural component exhibits statistically significant (α = 5%) periodicities associated with local rainfall variability linked to the El Niño-Southern Oscillation (ENSO), changes in the South American Convergence Zone (SACZ), and solar activity. These forcings drive erosional processes and influence sediment production that contribute naturally to the metallic element content in this tropical humid region where chemical weathering prevails.