This dataset reports continuous atmospheric measurements of CO2 from two receptor sites and three boundary sites in and around Boston, Massachusetts, USA, that were combined with high-resolution CO2 emissions estimates and the Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model to estimate regional CO2 emissions from September 2013 to December 2014. The HYSPLIT model followed an ensemble of 1,000 particles released at the urban CO2 measurement sites backward in time based on wind fields and turbulence from the North American Mesoscale Forecast System (NAM) at 12-km resolution to the boundary CO2 measurement sites to derive footprint values and CO2 enhancements expected from the prior emissions based on the Anthropogenic Carbon Emissions System (ACES) inventory and the urban-Vegetation Photosynthesis Respiration Model (urbanVPRM). This dataset contains three sets of data products: (1) observed hourly mean CO2 observations for two urban receptor sites in Boston, MA (Boston University (BU) and Copley Square (COP)), (2) observed hourly mean CO2 and calculated vertical profiles (50 - 5000 m) for three boundary sites around Boston including Harvard Forest at Petersham, MA (HF), Canaan, NH (CA), and Martha's Vineyard, MA (MVY), and modeled mean boundary CO2 concentrations for particles released from BU and COP, and (3) particle trajectory files including footprint values and CO2 enhancements above boundary CO2 concentrations from the HYSPLIT model.