Abstract Two sediment sections are investigated at Cape Arkhangelos, island of Rhodes, where Pleistocene marine sediments crop out in horsts and grabens of a Mesozoic basement. There, hemipelagic sediments characterized by upper bathyal communities are atypically mixed with much shallower faunal components because they were deposited close to rugged coastal landforms. Biostratigraphic analyses show that the sections were deposited between 1.8 and 0.9 Ma, and between 1.8 and 1.6 Ma, respectively. By combining the planktonic/benthic foraminiferal ratio with 31 bathymetric indicators chosen among extant species of benthic foraminifera, mollusks, and bryozoans, we show that relative sea-level fluctuations can be reconstructed in these atypical settings despite the proximity of steep slopes that favored transportation of allochthonous fauna. The shallow-water components (including gravels and calcareous algae) were transported downslope by the combined action of gravity, currents, and tectonic disturbance that promoted drowning (with a maximum flooding recorded at ca. 1.7 Ma) and then uplift of fault-bounded paleovalleys that formed during the Early Pleistocene. Abrupt facies changes and age differences between sections have been triggered by the irregular paleotopography of the Mesozoic basement, which fostered differential depositional settings, with outer to middle neritic deposits above the horsts and upper bathyal deposits in paleovalleys.