Stable isotopes have emerged as popular study targets when investigating emission of methane (CH₄) from lakes. Yet little is known on how isotopic patterns conform to variations in emission magnitudes—a highly relevant question. Here, we present a large multiyear data set on stable isotopes of CH₄ ebullition (bubbling) from three small adjacent subarctic lakes. The δ¹³C‐CH₄ and δD‐CH₄ range from −78.4‰ to −53.1‰ and from −369.8‰ to −218.8‰, respectively, and vary greatly among the lakes. The signatures suggest dominant hydrogenotrophic methanogenesis, particularly in the deep zones, but there are also signals of seemingly acetoclastic production in some high fluxing shallow areas, possibly fueled by in situ vegetation, but in‐sediment anaerobic CH₄ oxidation cannot be ruled out as an alternative cause. The observed patterns, however, are not consistent across the lakes. Neither do they correspond to the spatiotemporal variations in the measured bubble CH₄ fluxes. Patterns of acetoclastic and hydrogenotrophic production plus oxidation demonstrate that gains and losses of sediment CH₄ are dominated by sub‐lake scale processes. The δD‐CH₄ in the bubbles was significantly different depending on measurement month, likely due to evaporation effects. On a larger scale, our isotopic data, combined with those from other lakes, show a significant difference in bubble δD‐CH₄ between postglacial and thermokarst lakes, an important result for emission inventories. Although this characteristic theoretically assists in source partitioning studies, most hypothetical future shifts in δD‐CH₄ due to high‐latitude lake area or production pathway are too small to lead to atmospheric changes detectable with current technology.