In order to examine coastal changes during the Holocene, two sediment cores were collected from similar depths (36 m) located 10 km from one another, 3.6 km offshore of Ashkelon and Ashdod, and analyzed for granulometry, marine biomarkers, and element composition. Concurrent geophysical mapping showed that while the surface bathymetry of both locations is similar today, one core was positioned in the center of a former channel-like structure, and the other was positioned along a plateau. The results show a sequence of changes in both cores that generally trend from coarser, shallow-shelf characteristics to deeper-shelf characteristics. The overall estimated average sediment accumulation rates of both cores were similar, and three general phases could be defined (shallow phase, transitional phase, and deeper phase). However, the “channel” core exhibited higher complexity and variation within each phase, including the interpreted preservation of a larger number of high-energy events characterized by increased coarse shell content and larger grain sizes. The channel core also contained more bryozoan remains throughout, with the highest concentrations during the shallower phases. The plateau core values were more consistent per phase, with two distinctive anomalous layers that correlated with similar anomalies in the channel core. The results from this study contribute to the understanding of comparative depositional processes present on the shelf and how they vary as a reflection of morphological characteristics and water depth.