Complex terrain covers the vast majority of the Earth surface and affects local thermal wind flows by adding a gravitational component to the dynamics responding to local pressure gradients. The Leman Lake region, in Switzerland, thanks to its mountaineous topography, the presence of a large alpine lake and of two major cities (Lausanne and Geneva), represents an ideal testbed for studying the interaction between urban environments and lake breeze flows in complex terrain. However, most of the research investigating local fluid dynamics in the area predominantly focuses on the impact of wind flow on internal lake circulations, and limited attention has so far been given to the environmental impact of urban areas. Here, we use a set of high-resolution Weather Research and Forecast (WRF) model simulation experiments to investigate the diurnal and seasonal evolution of boundary layer dynamics in the Leman Lake region, with a focus on the environmental impacts associated with the cities of Lausanne and Geneva. In order to isolate urban impacts and explore the role of different land cover types, we compare simulation results from an “Urban” scenario featuring a realistic landscape representation, with simulation results from an hypothetical “Rural” scenario where urban areas are replaced by croplands. We also use an additional set of monthly simulations, to evaluate the potential for improved representation of physical processes offered by the integrated 1-D WRF Lake model. Analysis of results shows that urban environments, although of limited extent, are able to modify wind flows locally, e.g., by anticipating the diurnal onset of the lake breeze circulation. In turn, wind flows interact with local UHIs by advecting heat over the Leman Lake, in accordance with what has been observed by similar studies in world regions charaterized by different topographical and climatological conditions.