Stable isotopic analysis is a popular method to understand the mechanisms sustaining methane (CH4) emissions in various aquatic environments. Yet, the general lack of concurrent measurements of isotopes and fluxes impedes our ability to establish a connection between the variation in the rates of CH4 emission and isotopic signature. Here, we examine the magnitude of CH4 ebullition (bubbling) and stable carbon isotopic signature (δ13C-CH4) of bubble CH4 in four northern temperate lakes and evaluate the in-lake processes shaping their variability. The ebullitive CH4 flux and bubble δ13C-CH4 varied from 0.01 to 37.0 mmol m−2 d−1 and between −71.0‰ and −50.9‰, respectively. The high emission lakes in general and high fluxing shallow zones within each lake consistently showed enriched δ13C-CH4 signature. Subsequently, in addition to the temperature dependence (1.4 ± 0.1 eV), the rates of ebullition strongly correlated with the variability of δ13C-CH4 across our study lakes. Our results suggest that higher ebullitive emissions are sustained by acetoclastic methanogenesis, likely fueled by fresh organic matter inputs. Further, the annual whole-lake estimate of bubble isotopic flux alone showed depleted δ13C-CH4 values (−64.6 ± 0.6‰ to −60.1 ± 3.2‰), yet the signature of the total CH4 emission (ebullition + diffusion) was relatively enriched (−60.7‰ to −52.6‰) due to high methanotrophic activity in the water column. We show that δ13C-CH4 signature of bubbles can be linked to the magnitude of ebullition itself, yet we suggest there is a need to account for different emission pathways and their isotopic signature to allocate CH4 source signature to northern lakes.