Mesoscale models, such as the Weather Research and Forecasting (WRF) model, are increasingly used for high resolution simulations, particularly in complex terrain, but errors associated with terrain-following coordinates degrade the accuracy of the solution. Use of an alternative Cartesian gridding technique, known as an immersed boundary method (IBM), alleviates coordinate transformation errors and eliminates restrictions on terrain slope which currently limit mesoscale models to slowly varying terrain. In this dissertation, an immersed boundary method is developed for use in numerical weather prediction. Use of the method facilitates explicit resolution of complex terrain, even urban terrain, in the WRF mesoscale model. First, the errors that arise in the WRF model when complex terrain is present are presented. This is accomplished using a scalar advection test case, and comparing the numerical solution to the analytical solution. Results are presented for different orders of advection schemes, grid resolutions and aspect ratios, as well as various degrees of terrain slope. For comparison, results from the same simulation are presented using the IBM. Both two-dimensional and three-dimensional immersed boundary methods are then described, along with details that are specific to the implementation of IBM in the WRF code. Our IBM is capable of imposing both Dirichlet and Neumann boundary conditions. Additionally, a method for coupling atmospheric physics parameterizations at the immersed boundary is presented, making IB methods much more functional in the context of numerical weather prediction models. The two-dimensional IB method is verified through comparisons of solutions for gentle terrain slopes when using IBM and terrain-following grids. The canonical case of flow over a Witch of Agnesi hill provides validation of the basic no-slip and zero gradient boundary conditions. Specified diurnal heating in a valley, producing anabatic winds, is used to validate the use of flux (non-zero) boundary conditions. This anabatic flow set-up is further coupled to atmospheric physics parameterizations, which calculate surface fluxes, demonstrating that the IBM can be coupled to various land-surface parameterizations in atmospheric models. Additionally, the IB method is extended to three dimensions, using both trilinear and inverse distance weighted interpolations. Results are presented for geostrophic flow over a three-dimensional hill. It is found that while the IB method using trilinear interpolation works well for simple three-dimensional geometries, a more flexible and robust method is needed for extremely complex geometries, as found in three-dimensional urban environments. A second, more flexible, immersed boundary method is devised using inverse distance weighting, and results are compared to the first IBM approach. Additionally, the functionality to nest a domain with resolved complex geometry inside of a parent domain without resolved complex geometry is described. The new IBM approach is used to model urban terrain from Oklahoma City in a one-way nested configuration, where lateral boundary conditions are provided by the parent domain. Finally, the IB method is extended to include wall model parameterizations for rough surfaces. Two possible implementations are presented, one which uses the log law to reconstruct velocities exterior to the solid domain, and one which reconstructs shear stress at the immersed boundary, rather than velocity. These methods are tested on the three-dimensional canonical case of neutral atmospheric boundary layer flow over flat terrain.