AbstractThe presence of wave‐like structures in the planetary boundary layer and their influence on the scalar fluxes and on the surface energy balance were investigated analyzing one year of continuous measurements collected in southern Brazil. Submeso oscillating patterns in the wind velocity components, temperature and scalar (CO, HO) concentrations were isolated using their auto‐correlation functions. The analysis showed that low wind speeds are necessary to trigger wavy motions. During night‐time, in the presence of large vertical temperature gradients, horizontal meandering and internal gravity waves are dominant features of the stable boundary layer. Furthermore, a significant number of meandering cases were identified also during daytime in neutral conditions associated with low values of net radiation. One case‐study showed how, during daytime, the wave‐like patterns may be triggered by variations in the net radiation. Spectral analysis on the whole dataset showed that oscillations in the wind velocity and temperature field are frequently associated with CO and HO wavy patterns with similar time‐scales. These non‐turbulent oscillations produce unpredictable large‐scale contributions to vertical fluxes of temperature and scalar concentrations. The energy budget analysis showed how the choice of a proper averaging time filters out these contributions and improves the energy budget closure, as well as the estimation of the net ecosystem exchange. The results confirm the influence of submeso motions in scalar dispersion, flux patterns and surface energy balance during low wind speed conditions and stable stratification.