Processes regulating the rate of oxygen depletion determine whether hypoxia occurs and the extent to which greenhouse gases accumulate in seasonally ice-covered lakes. Here, we investigate the oxygen budget of four arctic lakes using high-frequency data during two winters in three shallow lakes (9–13 m maximal depth) and four winters in 24 m deep main basin of Toolik Lake. Incubation experiments measured sediment metabolism. Volume-averaged oxygen depletion measured in situ was independent of water temperature and duration of the ice-covered period. Average rates were between 0.2 and 0.39 g O2 m−2 d−1 in the shallow lakes and between 0.03 and 0.14 g O2 m−2 d−1 in Toolik Lake, with higher rates in smaller lakes with their larger sediment area to volume ratio. Rates decreased to ~ 20%–50% of initial values in late winter in the shallow lakes but less or not at all in Toolik. The lack of a decline in Toolik Lake points to continued oxygen transport to the sediment–water interface where oxygen consumption occurs. In all lakes, lower in situ oxygen depletion than in incubation measurements points toward increasing anoxia in the lower water column depressing loss rates. In Toolik, oxygen loss during early winter was less in years with minimal snow cover. Penetrative convection occurred, which could mix downwards oxygen produced by photosynthesis or excluded during ice formation. Estimates of these terms exceeded photosynthesis measured in sediment incubations. Modeling under ice-oxygen dynamics requires consideration of optical properties and biological and transport processes that modify oxygen concentrations and distributions.

Abstract: Floodplain lakes are widespread and ecologically important throughout tropical river systems, however data are rare that describe how temporal variations in hydrological, meteorological and optical conditions moderate stratification and mixing in these shallow lakes. Using time series measurements of meteorology and water‐column temperatures from 17 several day campaigns spanning two hydrological years in a representative Amazon floodplain lake, we calculated surface energy fluxes and thermal stratification, and applied and evaluated a 3‐dimensional hydrodynamic model. The model successfully simulated diel cycles in thermal structure characterized by buoyancy frequency, depth of the actively mixing layer, and other terms associated with the surface energy budget. Diurnal heating with strong stratification and nocturnal mixing were common; despite considerable heat loss at night, the strong stratification during the day meant that mixing only infrequently extended to the bottom at night. Simulations indicated that the diurnal thermocline up and downwelled creating lake‐wide differences in near‐surface temperatures and mixing depths. Infrequent full mixing creates conditions conducive to anoxia in these shallow lakes given their warm temperatures.