Abstract. In order to use high resolution in-situ measurements to constrain regional emissions of carbon dioxide (CO₂), we use a Lagrangian methodology based on diffusive backward trajectory tracer reconstructions. We use aircraft, tall tower and ground sites for CO₂ data collected nearby the CO₂ emission hot spot of the Tokyo Bay Area during the CONTRAIL campaign, from the MRI/JMA Tsukuba tall tower and from the World Data Centre for Greenhouse Gases (WDCGG). We calculated Bayesian inversions based on EDGAR 4 and CDIAC a priori fluxes. Estimated fluxes for the Tokyo Bay Area for the analyzed period between 2005 and 2009 range between 4.80×10⁻⁷ and 3.45×10⁻⁶ kg_CO2 m² s⁻¹ with significant time variations. Significant differences in retrieved fluxes of up to 21% were found when CONTRAIL measurements were added to the dataset. No significant trend was found in the time series of spatially averaged retrieved fluxes.