Microorganisms are ubiquitous in deep subsurface environments, but their role in the global carbon cycle is not well-understood. The natural abundance δ¹³C and Δ¹⁴C values of microbial membrane phospholipid fatty acids (PLFAs) were measured and used to assess the carbon sources of bacteria in sedimentary and granitic groundwaters sampled from three boreholes in the vicinity of the Tono Uranium Mine, Gifu, Japan. Sample storage experiments were performed and drill waters analyzed to characterize potential sources of microbial contamination. The most abundant PLFA structures in all waters sampled were 16:0, 16:1ω7c, cy17:0, and 18:1ω7c. A PLFA biomarker for type II methanotrophs, 18:1ω8c, comprised 3% and 18% of total PLFAs in anoxic sedimentary and granitic waters, respectively, sampled from the KNA-6 borehole. The presence of this biomarker was unexpected given that type II methanotrophs are considered obligate aerobes. However, a bacterium that grows aerobically with CH₄ as the sole energy source and which also produces 56% of its total PLFAs as 18:1ω8c was isolated from both waters, providing additional evidence for the presence of type II methanotrophs. The Δ¹⁴C values determined for type II methanotroph PLFAs in the sedimentary (−861‰) and granite (−867‰) waters were very similar to the Δ¹⁴C values of dissolved inorganic carbon (DIC) in each water (∼−850‰). This suggests that type II methanotrophs ultimately derive all their carbon from inorganic sources, whether directly from DIC and/or from CH₄ produced by the reduction of DIC. In contrast, δ¹³C values of type II PLFAs in the sedimentary (−93‰) and granite (−60‰) waters indicate that these organisms use different carbon assimilation schemes in each environment despite very similar δ13CCH4 values (∼−95‰) for each water. The δ¹³C_PLFA values (−28‰ to −45‰) of non-methanotrophic bacteria in the KNA-6 LTL water do not clearly distinguish between heterotrophic and autotrophic metabolisms, but Δ¹⁴C_PLFAvalues indicate that >65% of total bacteria filtered from the KNA-6 LTL water are heterotrophs. Ancient Δ¹⁴C values (∼−1000‰) of some PLFAs suggest that many heterotrophs utilize ancient organic matter, perhaps from lignite seams within the sedimentary rocks. The more negative range of δ¹³C_PLFA values determined for the KNA-6 granitic water (−42‰ to −66‰) are likely the result of a microbial ecosystem dominated by chemolithoautotrophy, perhaps fuelled by abiogenic H₂. Results of sample storage experiments showed substantial shifts in microbial community composition and δ¹³C_PLFAvalues (as much as 5‰) during 2–4 days of dark, refrigerated, aseptic storage. However, water samples collected and immediately filtered back in the lab from freshly drilled MSB-2 borehole appeared to maintain the same relative relationships between δ¹³C_PLFA values for sedimentary and granitic host rocks as observed for samples directly filtered under artesian flow from the KNA-6 borehole of the Tono Uranium Mine.