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In situ flux estimates reveal large variations in methane flux across the bottom boundary layer of a eutrophic lake

Methane (CH4) produced in anoxic sediments plays a significant role in the carbon economy of many lakes and reservoirs. CH4 released from sediments first crosses the bottom boundary layer (BBL), the layer of water overlying the lakebed where currents are slowed by friction with the sediments below. Physical and biogeochemical conditions in the BBL, which can fluctuate hourly to daily with basin‐wide internal waves (seiches), likely influence CH4 transport from sediments into the hypolimnion. In this study, we estimated CH4 fluxes across the BBL of a eutrophic lake using a novel in situ flux gradient approach adapted from marine applications. For 2–6 h periods throughout the spring and summer, we estimated CH4 fluxes across the BBL using simultaneous measurements of CH4 concentrations, turbulent mixing, and thermal stratification. Sub‐daily variation in CH4 fluxes was high, and CH4 fluxes sometimes changed several‐fold within hours. These rapid shifts in BBL fluxes were likely influenced by fluctuations in seiche‐driven variations in the intensity of BBL turbulent mixing. Fluxes increased from spring to summer, concurrent with the development of lake stratification, and fueled an accumulation of CH4 below the thermocline. Throughout the summer, CH4 flux across the BBL exceeded CH4 accumulation below the thermocline, suggesting significant methanotrophy in the hypolimnion, consistent with incubation‐based oxidation rates. Our results are the first to demonstrate sub‐daily and seasonal variability in the timing and magnitude of CH4 fluxes within a lake BBL, and highlight a need to quantify such variability in other lentic systems.