As city governments take steps towards establishing emissions reduction targets, the atmospheric research community is increasingly able to assist in tracking emissions reductions. Researchers have established systems for observing atmospheric greenhouse gases in urban areas with the aim of attributing greenhouse gas concentration enhancements (and thus, emissions) to the region in question. However, to attribute enhancements to a particular region, one must isolate the component of the observed concentration attributable to fluxes inside the region by removing the background, which is the component due to fluxes outside. In this study, we demonstrate methods to construct several versions of a background for our carbon dioxide and methane observing network in the Washington, DC and Baltimore, MD metropolitan region. Some of these versions rely on transport and flux models, while others are based on observations upwind of the domain. First, we evaluate the backgrounds in a synthetic data framework, then we evaluate against real observations from our urban network. We find that backgrounds based on upwind observations capture the variability better than model-based backgrounds, although care must be taken to avoid bias from biospheric carbon dioxide fluxes near background stations in summer. Model-based backgrounds also perform well when upwind fluxes can be modeled accurately. Our study evaluates different background methods and provides guidance determining background methodology that can impact the design of urban monitoring networks.