Syndepositional diagenesis is a complicating factor when interpreting geochemical proxies in carbonate sedimentary environments. Previous studies have suggested that carbonate deposits may preserve the geochemical and isotopic signatures of seawater that can be used for paleo-redox reconstructions. However, more work is necessary to understand how these trace metals are preserved. The present study examines shallow marine carbonate sediments from the Bahamas to better understand diagenetic effects on trace metal uptake and sequestration. Analysis of diagenetic effects and trace metal uptake follows a multi-method approach, combining sequential extraction, stable isotope analyses, and rare earth elemental analysis. Stable isotopes track bacterial sulfate reduction, denitrification, and organic matter source and provide insight into thresholds and processes for the authigenic trace metal uptake. Importantly, exchangeable phases exhibit authigenic accumulation of molybdenum, uranium and vanadium, and intensified bacterial sulfate reduction is evidenced by most depleted sulfur isotope signatures. In addition, rare earth element values are very indicative proxies that suggest altered primary seawater trace element in carbonates (no cerium or lanthanum anomaly, moderate heavy rare earth element enrichment, decreased y/ho ratios and positive correlations between aluminum, manganese, and iron). Taken together, these results allow the development of a framework to better understand how to apply sedimentary geochemistry of carbonate rocks to paleo-environments as this study shows significant authigenic accumulation of redox-sensitive trace metals by exchangeable phases.