The wavelet-based eddy capturing approach is extended to three-dimensional bluff body flows, where the flow geometry is enforced through Brinkman volume penalization. The wavelet-collocation/volume-penalization combined method is applied to the simulation of vortex shedding flow behind an isolated stationary prism with square cross-section. Wavelet-based direct numerical simulation is conducted at low supercritical Reynolds number, where the wake develops fundamental three-dimensional flow structures, while wavelet-based adaptive large-eddy simulation supplied with the one-equation localized dynamic kinetic-energy-based model is performed at moderately high Reynolds number. The present results are in general agreement with experimental findings and numerical solutions provided by classical non-adaptive methods. This study demonstrates that the proposed hybrid methodology for modelling bluff body flows is feasible, accurate and efficient.