This presentation covers recent advances in Variational Multiscale (VMS) formulation for modeling environmental flows using both finite-elements (FEM) and isogeometric analysis (IGA). The flow is modeled using the Navier-Stokes equations for incompressible stratified flows with the Boussinesq approximation, incorporating an additional advection-diffusion equation for the temperature/density field. Weakly imposed Dirichlet boundary condition for velocity and temperature/density is used to capture flow behaviour near the wall without the need to use extra fine meshes. Various wall modeling techniques is also discussed, including surface roughness. The accuracy and robustness of the formulation is shown on various 3D cases including stratified channel flow, flow over complex topography, wind farm modeling and other. Comparisons with field data, laboratory experiments, and high-fidelity simulations like DNS and LES demonstrate the framework's ability to accurately capture phenomena such as intermittent turbulence, low-level jets, and flow separation.