Abstract. A millimetre-wave scintillometer was paired with an infrared scintillometer enabling estimation of large-area evaporation across northern Swindon, a suburban area in the UK. Both sensible and latent heat fluxes can be obtained using this technique, as it is able to provide both temperature and humidity structure parameters, offering a major advantage over conventional single-wavelength scintillometry. The first paper of this two-part series presented the measurement theory and results of the structure parameters. In this second paper, heat fluxes are obtained and analysed. These fluxes, estimated using two-wavelength scintillometry over an urban area, are the first of their kind. Source area modelling suggests the scintillometric fluxes are representative of 5–10 km2. For comparison, local-scale (0.05–0.5 km2) fluxes were measured by an eddy covariance station. Similar responses to seasonal changes are evident at the different scales but the energy partitioning varies between source areas. The response to moisture availability is explored using data from two consecutive years with contrasting rainfall patterns (2011–2012). This extensive dataset offers insight into urban surface–atmosphere interactions and demonstrates the potential for two-wavelength scintillometry to deliver fluxes over mixed land cover, typically representative of an area 1–2 orders of magnitude greater than for eddy covariance measurements. Fluxes at this scale are extremely valuable for hydro-meteorological model evaluation and assessment of satellite data products.