Iron-rich, ferruginous waters were the dominant geochemical regime for most of Earth's history. Modern ferruginous waters are found in stratified, sulfur-poor lakes, and serve as crucial analogs for biogeochemical cycling throughout Earth's past. Here we present the first depth-resolved data of physical structure, nutrients and trace elements from Lake Poso (Indonesia), a deep oligotrophic ancient lake. Lake Poso is ferruginous, with anoxia below ~ 90 m depth, placing it among the world's largest ferruginous lakes. Physical stratification is weaker than other tropical anoxic lakes, indicating sensitivity for paleoclimate reconstructions. Trace elements and nutrients are predominantly shaped by the oxic–anoxic transition. Manganese– and Fe oxyhydroxide–driven biogeochemical cycling occurs at distinct depth horizons, with Co and Ni controlled by Mn and showing shallow release in anoxic waters, while V, Cr, P, and As are controlled by Fe, with release in surface sediments and diffusive transport. Chromium is nonquantitatively removed in anoxic waters, in contrast to widespread assumptions in Cr-based paleoreconstructions. Oxycline U and Se removal corresponds to a local N minimum, suggesting biological reduction and/or uptake. These first ferruginous water Se data also show removal in sediments, indicating sediment signals reflect multiple removal processes and informing Se-based paleoreconstructions, while the absence of sediment U removal contrasts other anoxic basins. A comparison with other ferruginous lakes demonstrates how local influences drive deviations from expectations in other systems, and highlight common, generalizable ferruginous basin features. Therefore, these data will guide research in ferruginous settings across space and time, and improve paleoreconstructions from ferruginous sediment records.