The propagation of shear waves in an anisotropic fluid saturated porous layer over a prestressed semi-infinite homogeneous elastic half-space lying under an elastic homogeneous layer with irregularity present at the interface with rigid boundary has been studied. The rectangular irregularity has been taken in the half-space. The dispersion equation for shear waves is derived by using the perturbation technique followed by Fourier transformations. The dimensionless phase velocity is plotted against dimensionless wave number for the different size of ratios of depth of rectangular irregularity with the height of the layer and anisotropy parameters with the help of MATLAB graphical routines in presence and absence of initial stress. From the graphical results, it has been seen that the phase velocity is significantly influenced by the wave number, the depth of the irregularity, rigid boundary and initial stress. The acquired outcomes can be valuable for the investigation of geophysical prospecting and understanding the cause and evaluating of damage due to earthquakes.