Abstract. Understanding the boundary layer dynamics over urban areas is important to improve estimates of the emissions of greenhouse gases (GHG), and predict their atmospheric mole fractions in these areas. Here we present the results of the annual vertical profiling measurement campaign performed in Krakow (Southern Poland). The campaign consisted of 12 monthly-based diurnal measurements of CO2 and CH4 molar fraction vertical profiles supplemented by meteorological parameters focused on the investigation of the dynamics of nocturnal boundary layer vertical structure within the urban boundary layer. The profile data were collected using two platforms: (i) a tethered touristic balloon operating commercially in the city centre and (ii) a drone system, with the selection of the platform based on operational availability and meteorological conditions. CO2 and CH4 molar fractions were measured using Picarro G2311-f (Picarro Inc., Santa Clara, California, USA) cavity ring-down spectrometer, while the meteorological conditions along the profile were measured using a set of temperature, relative humidity, pressure and wind low-cost sensors dedicated for application on-board of UAV platforms. The obtained results allowed us to analyse in-depth the formation, development and disappearance of the nocturnal boundary layer. In selected profiles, a CO2 and CH4 plumes located over the inversion layer (150–250 m AGL) were detected during the nighttime and morning hours. The application of high-resolution numerical simulations using the WRF-GHG model made it possible to identify the source of CO2 plume as a power plant located ca. 10 km southwest of the balloon launch location.