A modified set of governing differential equations for geophysical fluid flows is derived. All of the simulation fields are decomposed into a nominal large-scale background state and a small-scale perturbation from this background, and the new system is closed by the assumption that the perturbation is one-way coupled to the background. The decomposition method, termed the multi-scale localized perturbation method (MSLPM), is then applied to the governing equations of stratified fluid flows, implemented in OpenFOAM, and exercised in order to simulate the interaction of a vertically-varying background shear flow with an axisymmetric perturbation in a turbulent ocean environment. The results demonstrate that the MSLPM can be useful in visualizing the evolution of a perturbation within a complex background while retaining the complex physics that are associated with the original governing equations. The simulation setup may also be simplified under the MSLPM framework. Further applications of the MSLPM, especially to multi-scale simulations that encompass a large range of spatial and temporal scales, may be beneficial for researchers.