Decreasing duration and occurrence of northern hemisphere ice cover due to recent climate warming is well-documented; however, biogeochemical dynamics underneath the ice are poorly understood. We couple time-series analyses of water column and sediment water interface (SWI) geochemistry with hydrodynamic data to develop a holistic model of iron (Fe), manganese (Mn), and phosphorus (P) behavior underneath the ice of a shallow eutrophic freshwater bay. During periods of persistent subfreezing temperatures, a highly reactive pool of dissolved and colloidal Fe, Mn, and P develops over time in surface sediments and bottom waters due to reductive dissolution of Fe/Mn(oxy)hydroxides below the SWI. Redox dynamics are driven by benthic O2 consumption, limited air–water exchange of oxygen due to ice cover, and minimal circulation. During thaw events, the concentration, distribution and size partitioning of all species changes, with the highest concentrations of P and “truly dissolved” Fe near the water column surface, and a relatively well-mixed “truly dissolved” Mn and “colloidal” Fe profile due to the influx of geochemically distinct river water and increased circulation. The partitioning and flux of trace metals and phosphorus beneath the ice is dynamic, and heavily influenced by climate-dependent physical processes that vary in both time and space.