Objective <p>Assessments concerning the quality of sediments under the influence of shrimp farming activities in the Lower São Francisco River region in Brazil have become paramount due to the significant growth of this activity in that region. In this sense, this study aimed to evaluate metal chemical profiles in sediment cores from three shrimp farms located in the Lower São Francisco River.</p> Methods <p>Both partial extraction and total digestion methods were applied to determine Ca, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, and Zn, as well as organic matter content, in sediment cores collected from three shrimp farms. Chemical analysis was performed using inductively coupled plasma optical emission spectrometry (ICP OES). Multivariate analysis was conducted to investigate geochemical sediment profile patterns. Pollution indices and sediment quality guidelines were also assessed.</p> Results <p>The highest metal concentrations (Cr, Cu, Mn, Ni, Zn) were observed in the surface sediment layers, especially in the drainage channel samples. Organic matter content varied significantly, with higher values detected near mangroves. A principal component analysis and hierarchical cluster analysis identified metal clusters associated with factors such as salinity and shrimp farming management. In general, the calculated pollution indices and sediment quality guidelines indicate that the investigated metals are below critical limits.</p> Conclusion <p>This study verified that the presence of the analyzed chemical elements in the core sediments from three shrimp farms in the Lower São Francisco River region are mainly due to shrimp feed, which is influenced by granulometry and organic matter. The detected concentrations, however, do not present significant ecological risks when considering the calculated pollution indices.</p>