In high-pH ($\text{pH}>10$) fluids that have participated in low-temperature ($<150\,^{\circ}\text{C}$) serpentinization, the dominant form of C is often methane (CH$_{4}$), but the origin of this CH$_{4}$ is uncertain. To assess CH$_{4}$ origin during low-temperature serpentinization, we pumped fluids from aquifers within the Samail Ophiolite, Oman. We determined fluid chemical compositions, analyzed taxonomic profiles of fluid-hosted microbial communities, and measured isotopic compositions of hydrocarbon gases. We found that 16S rRNA gene sequences affiliated with methanogens were widespread in the aquifer. We measured clumped isotopologue ($^{13}$CH$_{3}$D and $^{12}$CH$_{2}$D$_{2}$) relative abundances less than equilibrium, consistent with substantial microbial CH$_{4}$ production. Further, we observed an inverse relationship between dissolved inorganic C concentrations and $\delta^{13}\text{C}_{\text{CH}_{4}}$ across fluids bearing microbiological evidence of methanogenic activity, suggesting that the apparent C isotope effect of microbial methanogenesis is modulated by C availability. A second source of CH$_{4}$ is evidenced by the presence of CH$_{4}$-bearing fluid inclusions in the Samail Ophiolite and our measurement of high $\delta^{13}\text{C}$ values of ethane and propane, which are similar to those reported in studies of CH$_{4}$-rich inclusions in rocks from the oceanic lithosphere. In addition, we observed 16S rRNA gene sequences affiliated with aerobic methanotrophs and, in lower abundance, anaerobic methanotrophs, indicating that microbial consumption of CH$_{4}$ in the ophiolite may further enrich CH$_{4}$ in $^{13}$C. We conclude that substantial microbial CH$_{4}$ is produced under varying degrees of C limitation and mixes with abiotic CH$_{4}$ released from fluid inclusions. This study lends insight into the functioning of microbial ecosystems supported by water/rock reactions.