Quantifying sector-resolved methane fluxes in complex emissions environments is challenging yet necessary for inventory validations.  We separate energy and agriculture sector methane using a dynamic linear model of methane, ethane, and ammonia mixing ratios measured at a Northern Colorado site from November 2021 to January 2022. Combining observations with spatially resolved inventories and inverse methods, energy and agriculture methane fluxes are constrained across a ~850 km² area. Optimized energy sector fluxes were 22% lower than the inventory despite a ~360% increase in regional energy production since the inventory was constructed, suggesting a regional decline in emissions factors. In contrast, optimized agriculture fluxes were 3× larger than the inventory; we demonstrate this discrepancy is consistent with the spatial distribution of agricultural sources. These results highlight the utility of sector-apportioned methane observations for multi-sector inventory optimization in complex environments, which may prove valuable for national and global quantification of sector-resolved methane fluxes.