A large-eddy simulation (LES) tool is developed for simulating the dynamics of atmospheric boundary layers using lattice Boltzmann method (LBM), which is an alternative approach for computational fluid dynamics and proved to be very well suited for the simulation of low-Mach flows. The equations of motion are coupled with the global complex physical models considering the coupling among several mechanisms, namely basic hydro-thermodynamics and body forces related to stratification, Coriolis force, canopy effects, humidity transport and condensation. Mass and momentum equations are recovered by an efficient streaming, collision and forcing process within the framework of LBM while the governing equations of temperature, liquid and vapor water fraction are solved using a finite volume method. The implementation of wall models for atmospheric boundary layer, subgrid models and interaction terms related to multiphysic phenomena (e.g. stratification, condensation) is described, implemented and assessed in this study. An Immersed Boundary approach is used to handle flows in complex configurations, with application to flows in realistic urban areas. Applications to both wind engineering and atmospheric pollutant dispersion are illustrated.