Heterogeneous land-covers induce the formation of secondary flows and small-scale boundary layer processes. While turbulent fluxes over a continuous snow cover are mostly governed by the spatial variability of wind velocity and solar radiation, local advection of sensible heat and boundary layer decoupling become additionally important for the surface energy exchange over patchy snow covers. Furthermore, evolving katabatic and anabatic winds strongly change the mean flow patterns over snow free and snow covered areas causing positive and negative buoyancy production. In this study we use an atmospheric model (Advanced Regional Prediction System) to investigate boundary layer processes over patchy snow covers in an alpine catchment. The model is initialized with low to high snow cover ratios based on field measurements of snow distribution. We particularly analyse the effect of heat advection, boundary layer decoupling and changing patterns of secondary flows on the energy balance at the local and catchment scale. The numerical results show that the changing land-cover controls the length scale of internal boundary layers, while secondary flows drive the strength of boundary layer decoupling and heat advection. The relative importance of boundary layer processes depend on the snow patch size distribution and the synoptic wind. Stronger synoptic winds and low snow cover ratios increase the effect of heat advection and decrease the impact of boundary layer decoupling on the catchment`s melt behaviour. The typical lengths of stable internal boundary layers coincide with snow patch size distribution, which is consistent with typical length scales of snow accumulation patterns. As those length scales are in the order of tens of meters for the studied alpine catchment, very small grid sizes (below 10 m) are required to adequately model boundary layer processes which are shown to significantly alter the energy balance over patchy snow covers.