Methane is a greenhouse gas and is an important component of carbon cycling in freshwater environments. Isotope ratios of methane ( 13 C/ 12 C and D/H) are used extensively as tracers to identify methane sources. Recent advances in the measurement of clumped methane isotopologues ( 13 CH 3 D, 12 CH 2 D 2 ) offer new opportunities to constrain sources and sinks of atmospheric methane. Previous measurements of clumped methane isotopologues from freshwater environments have been spatially and temporally limited. The abundance of 13 CH 3 D and methane flux from ebullition in the deep basin of Upper Mystic Lake were measured from May to November 2021 to characterize the source isotopologue signatures and methane fluxes for midlatitude lakes. The trends in δ 13 C and δD values support decreased methane oxidation in the early summer compared to fall. The Δ 13 CH 3 D values from this study range from 2.0 to 4.2‰, reflecting methane oxidation occurring anaerobically in lake sediments and euxinic bottom waters at sample sites. The relatively large variation in the Δ 13 CH 3 D values observed within this lake basin aligns with previous observations of bubbles from arctic lakes. The values of Δ 13 CH 3 D do not correlate with methane flux, suggesting that Δ 13 CH 3 D measurements from background ebullition are not sensitive as a proxy for ebullition rates. This study presents a uniquely large (n = 40) set of freshwater Δ 13 CH 3 D values from a single lake basin, which we use to recommend a sampling strategy of ≥9 samples to constrain the Δ 13 CH 3 D source signal within ∼0.5‰ from similar environments. This data demonstrates the utility of clumped methane isotopologues to gain insights into local biogeochemical processes from field studies and points to the challenge of using clumped isotopologue measurements to constrain global freshwater−methane sources to the atmosphere.