This study investigates spatiotemporal dynamics in metal sedimentation in the North American Great Lakes and their underlying biogeochemical controls. Bulk geochemical and isotope analyses of n = 72 surface and core sediment samples show that metal (Cu, Zn, Pb) concentrations and their isotopic compositions vary spatially across oligotrophic to mesotrophic settings, with intra-lake heterogeneity being similar or higher than inter-lake (basin-scale) variability. Concentrations of Cu, Zn, and Pb in sediments from Lake Huron and Lake Erie vary from 5 to 73 mg/kg, 18–580 mg/kg, and 5–168 mg/kg, respectively, but metal enrichment factors were small (<2) across the surface- and core sediments. The isotopic signatures of surface sediment Cu (δ65Cu between −1.19‰ and +0.96‰), Zn (δ66Zn between −0.09‰ and +0.41‰) and Pb (206/207Pb from 1.200 to 1.263) indicate predominantly lithogenic metal sourcing. In addition, temporal trends in sediment cores from Lake Huron and Lake Erie show uniform metal concentrations, minor enrichment, and Zn and Pb isotopic signatures suggestive of negligible in-lake biogeochemical fractionation. In contrast, Cu isotopic signatures and correlation to chlorophyll and macronutrient levels suggest more differentiation from source variability and/or redox-dependent fractionation, likely related to biological scavenging. Our results are used to derive baseline metal sedimentation fluxes and will help optimize water quality management and strategies for reducing metal loads and enrichment in the Great Lakes and beyond.