Biological principles suggest that recorded species diversity should increase as sampled area and habitat diversity increase. However, the interactions between Earth system drivers of these physical quantities, their representation in the preserved rock record, and fossil species counts are debated. We tracked marine bedrock area, lithofacies diversity, and echinoid species diversity through an 80 m.y. sea-level cycle, as recorded in the Cretaceous of the United Kingdom, to test these relationships. Relative completeness of the rock record rises during transgression but drops rapidly at maximum flooding and continues to fall during highstand. Lithofacies diversity peaks during transgression but drops sharply as maximum flooding is reached, whereas bedrock area peaks at maximum flooding then declines progressively through the highstand interval as a result of post-Cretaceous erosion. Both bedrock area and number of lithofacies units correlate with species diversity, but species diversity is predicted best by the two combined. There are no simple relationships between bedrock area and lithofacies diversity or the original area of marine sediments and range of habitats that once existed; these variables are strongly shaped by stratigraphic architecture. While the geological record left by a major sea-level cycle accurately captures the biological evolution of local communities, it is incomplete and systematically biased in its coverage of environments and communities. Erosional truncation of sediment packages and species ranges in the later stages of sea-level cycles explains the reported asymmetric relationship between macroevolution and macrostratigraphy.