The simultaneous interaction of lake breeze (LB) flows, complex terrain circulations and urban environments has so far received limited attention in the scientific literature. Here, we use the Weather Research and Forecasting model to investigate the aero- and thermodynamical interaction between Lake Geneva, the Swiss cities of Lausanne and Geneva and their rugged alpine landscape. To better isolate the role of urban areas, we compare results from a set of year-long simulations representing both realistic urban and hypothetical rural landcover scenarios. The results show that the urban areas of Lausanne and Geneva have a negligible effect on the dynamical evolution of LB, mostly consisting of wind deceleration caused by increased surface drag. However, the daytime excess heat over Lausanne results in a shift of the local anabatic wind regime onset time, one hour ahead, and a 1 km spatial displacement northward of the location of opposing flow collision. Urban-induced changes in heat advection can further lead to warmer air temperatures over the lake or cooler urban conditions along the lake shore. Our study shows that, although with due magnitude differences, mid-sized cities may have similar effects on wind and heat dynamics as larger metropolises in different landscapes and climates. This article is part of the theme issue ‘Urban heat spreading above and below ground’.