Stylolites are tooth-like planar pressure solution features common in carbonate sedimentary rocks that cause intrinsic heterogeneities and result in boundary layers often parallel to bedding. As such they impact the propagation of acoustic waveforms and energy at the laboratory scale within the host rock matrix. Through a series of tests on cylindrical limestone samples with varying layers of stylolites, along with nondestructive computed tomography scanning and index tests, we assess the three-dimensional morphology and hardness of stylolites in comparison to the surrounding rock. Acoustic wave recordings examine how these stylolites affect transmitted waveform characteristics. Results indicate that stylolites acting as weakness discontinuities, exhibit minimal influence on the first arrivals of transmitted acoustic waveforms but significantly affect coda waves by reducing relative velocity and increasing wave attenuation. Numerical simulations confirm these findings. With increasing stylolite thickness and associated wave impedance reduction, acoustic waves scatter more strongly and introduce more noise into the wavefield, thus, impacting methodologies used for identifying source locations. In contrast, stylolite topography has a minimal effect on transmitted waveform properties. While the presence of stylolites has minimal effect on the first wave arrivals, it introduces noise in later arrivals. These results suggest that, at laboratory scale, Kirchhoff-based localization procedures may be preferable to full waveform alternatives for monitoring fracture propagation in rock samples with stylolites.