Numerous lakes worldwide are deteriorating due to climate change and other human impacts. Specifically, low dissolved oxygen levels are threatening food webs and water security. Protection, mitigation, and future projections of these phenomena call for a better understanding of their past evolution. For decades, paleolimnology has provided information about past environments by studying sediment structure and geochemistry. Among the latter, iron (Fe) and manganese (Mn), and their ratios are well-established proxies of the past water oxygenation. However, the understanding of redox-sensitive elements' mobility calls for a still scarce use of spatial approaches, complementing typical investigations focused on temporal geochemical variability. To address that, we began with 33-month-long observations of limnological conditions (water temperature and dissolved oxygen concentration) in a small, deep lake experiencing seasonal anoxia, continued with characterization of major sediment structures, and concluded with geochemical and statistical analyses of collected material. We used 31 surface samples from different depths and investigated their sediment structures, bulk geochemistry (CNS and biogenic silica), elemental composition (micro-X-ray fluorescence), and Fe and Mn fractions. Our data indicate clear, testable links between oxygen availability and sediment structures, as well as their chemical composition. Anoxia promotes the deposition and preservation of laminations. Whereas seasonally migrating oxycline drives geochemical focusing, enriching the deepest sediments in Fe and Mn. This proves that both Fe and Mn are reliable indicators of deep-water redox conditions. Our study bridges modern limnology and paleolimnology and emphasizes the need to treat lakes and their sediments as a complete, complex system.