Methane is a potent greenhouse gas that plays an important role in atmospheric chemistry and global warming. The current global methane budget has large uncertainties, and a better understanding of the budget would help to guide strategies for reducing anthropogenic emissions to fight climate change. Natural geologic methane emissions are a particularly poorly constrained source, with top-down estimates from ¹⁴C in ice cores suggesting much lower geologic emissions than bottom-up scaling of direct flux measurements. Our study aims to contribute to resolving this discrepancy through improved bottom-up characterization of geologic methane seepage in the San Juan Basin in southwestern Colorado and northwestern New Mexico, USA. We performed 983 new flux chamber measurements in this basin during summer 2022 and winter 2023 field campaigns. Our results, in combination with prior measurements, suggest that natural seepage in the San Juan Basin only occurs on or near the Fruitland coal outcrop. Specifically, our new measurements confirm previous measurements of seepage along the northwestern exposure of the Fruitland outcrop in Colorado (a known hydrodynamic overpressure region) and for the first time, identified seepage locations along the southernmost Fruitland outcrop exposure in New Mexico, in association with a coal cleat and a fault. Overall, seepage along the Fruitland coal outcrop is heterogeneously distributed, with both positive and negative (interpreted as microbial soil sink) methane fluxes. Features that are hypothesized to be predictive of seepage (e.g., faults) were not associated with positive methane fluxes in areas outside of the Fruitland outcrop. Our best estimate for total geologic methane seepage in the San Juan Basin from spatial interpolation and statistical upscaling is approximately 0.14 Tg CH₄/yr, with a range from 0.029 to 0.48 Tg CH₄/yr. This best-estimate value is lower than a previous bottom-up estimate from a gridded seepage inventory, but higher than a previous top-down estimate.