Biogeochemical dynamics under seasonal ice cover were investigated in the shallow (<10 m) water column of highly productive Georgetown Lake, western Montana, USA. This high altitude (1,800 m) reservoir is well-mixed in summer, but becomes strongly stratified under ice cover (mid-November–mid-May). A rapid drop in dissolved oxygen (DO) concentration and rise in dissolved inorganic carbon (DIC) concentration was observed after the onset of ice, with a corresponding increase in δ¹⁸O-DO and decrease in δ¹³C-DIC, likely caused by respiration (R) of organic carbon. Photosynthesis/respiration ratios (P/R) estimated from simultaneous measurement of DO and δ¹⁸O-DO were near unity prior to ice formation but then systematically decreased with time and depth in the lake under ice cover. P/R in the water column was higher at a shallower monitoring site compared to a deeper site near the dam outlet, which may have been important for over-winter survival of salmonids. By March, the bottom 3 m of the water column at both sites was anoxic, with the bottom 1 m being euxinic. Elevated concentrations of dissolved sulfide, ammonium, phosphate, Fe²⁺, and Mn²⁺ in deep water suggest coupling of organic carbon degradation with reduction of a number of electron acceptors (e.g., Fe³⁺, NO₋₃,SO₂₋₄). The concentrations and δ³⁴S values of H₂S in the deep water and SO₂₋₄ in the shallow water were similar, indicating near-complete reduction of sulfate in the euxinic zone. Late in the winter, an influx of isotopically heavy DIC was noted in the deep water coincident with a buildup of dissolved CH₄ to concentrations >1 mM. These trends are attributed to acetoclastic methanogenesis in the benthic sediments. This pool of dissolved CH₄ was likely released from the lake to the atmosphere during spring ice-off and lake turnover.