This paper describes process-based estimation of CH4 emissions from sources in Indianapolis, Indiana and compares these with atmospheric inferences of whole city emissions. Emissions from the natural gas distribution system were estimated from measurements at metering and regulating stations and from pipeline leaks. Tracer methods and inverse plume modeling were used to estimate emissions from the major landfill and wastewater treatment plant. These direct source measurements informed the compilation of a methane emission inventory for the city equal to 29 Gg/yr (5% to 95% confidence limits, 15 to 54 Gg/yr). Emission estimates for the whole city based on an aircraft mass balance method and from inverse modeling of CH4 tower observations were 41 ± 12 Gg/yr and 81 ± 11 Gg/yr, respectively. Footprint modeling using 11 days of ethane/methane tower data indicated that landfills, wastewater treatment, wetlands, and other biological sources contribute 48% while natural gas usage and other fossil fuel sources contribute 52% of the city total. With the biogenic CH4 emissions omitted, the top-down estimates are 3.5–6.9 times the nonbiogenic city inventory. Mobile mapping of CH4 concentrations showed low level enhancement of CH4 throughout the city reflecting diffuse natural gas leakage and downstream usage as possible sources for the missing residual in the inventory.