The specific problems of determining and simulating the surface energy balance (SEB) and the mixing height (MH) over urban areas are examined. The SEB and MH are critical components of algorithms and numerical models for the urban boundary layer, though the constituent parts of the SEB and the MH are not routinely measured by national weather services. Parameterisations are thus needed in applications. In this investigation, several recently developed algorithms and models for estimating the SEB and MH were applied to new datasets and assessed. Results are discussed in terms of the need for spatial resolution and the parameters needed to describe the urban atmosphere. Limitations of models are identified and recommendations for further development and observations are given. Having identified gaps in knowledge, key findings from new urban experiments and numerical modelling for the SEB and MH are given. The diurnal cycle for the SEB is significantly different from rural conditions—urban heat storage is needed in urban parameterisations. The urban MH is increased over the rural MH, as shown by several numerical schemes and careful sodar analyses. This work has been carried out within the COST-715 Action “Meteorology applied to urban air pollution problems (1998–2004). COST 715 reached a consensus proposing representatively sited measurements of meteorological parameters and turbulent fluxes above roof-tops, and recognised that such data are needed to improve numerical models of the urban surface processes.