Anthropogenic emissions of carbon dioxide (CO2) and methane (CH4) in the atmosphere constitute an important component of the related carbon budget. The main source of anthropogenic CO2 is burning of fossil fuels, especially in densely populated areas. Similar emissions of CH4 are associated with the agricultural sector, coal mining, and other human activities, such as waste management and storage and natural gas networks supplying methane to large urban, industrial centers. We discuss several methods aimed at characterizing and quantifying atmospheric loads and fluxes of CO2 and CH4 in Krakow, the second largest city in Poland. The methods are based on atmospheric observations of mixing ratios as well as isotopic composition of the investigated gases. Atmospheric mixing ratios of CO2 and CH4 were measured using gas chromatography (GC) and cavity ring-down spectroscopy (CRDS). The isotopic composition of CO2 and CH4 was analyzed using isotope ratio mass spectrometry (IRMS), accelerator mass spectrometry (AMS), and CRDS techniques. These data, combined with auxiliary information characterizing the intensity of vertical mixing in the lower atmosphere (height of the nocturnal boundary layer [NBL] and atmospheric 222Rn concentration), were further used to quantify emission rates of CO2 and CH4 in the urban atmosphere of Krakow. These methods provide an efficient way of quantifying surface emissions of major greenhouse gases originating from distributed sources, thus complementing the widely used bottom-up methodology based on emission statistics.