Although the paleontological effects of unconformities and changes in sedimentation rate are readily understood and widely appreciated, the importance of ecological gradients and their interplay with stratigraphic architecture is often overlooked. Although marine and nonmarine systems have multiple ecological gradients, the most important at the scale of a sedimentary basin are correlated with elevation and latitude, and also substrate consistency in marine environments. Elevation is correlated with distance from the coast in coastal nonmarine basins, and water depth is the equivalent of elevation in marine systems. Elevation is particularly important not just because it commonly constitutes 20–30% of the variance in community composition, but also because it changes predictably with sequence-stratigraphic architecture. As a result, fossil assemblages change stratigraphically even when ecosystem structure is relatively constant (i.e., minimal origination, extinction, immigration, and change in the ecological characteristics of species). Where ecological gradients are not recognized in the fossil record, stratigraphically generated changes in fossil assemblages, particularly abrupt ones, are likely to be misinterpreted as a perturbation of ecosystem structure, a situation that plagues most mass-extinction studies and possibly other biotic events such as evolutionary radiations and immigration events. Recognizing stratigraphically-generated changes in fossil assemblages is difficult partly because it requires training in depositional environments and sequence stratigraphy, but also because ecological gradients commonly require multivariate statistical methods to be described adequately. Moreover, although lithofacies commonly provide a proxy for water depth in marine systems, it is a crude yardstick. In nonmarine systems, elevation gradients commonly lack any lithofacies proxy, except for more hydromorphic paleosols in lower elevation settings. Elevational gradients in marine and nonmarine systems are expressed differently. In marine systems, species turnover is typically present across the gradient, usually at similar rates, although turnover can be heightened at some ecological transitions, such as with reefs. In nonmarine systems, turnover is typically more strongly developed within 20–50 km of the coast than in inland settings, where it may even be absent. Multiple types of surfaces generate abrupt changes in water depth in marine systems and, therefore, fossil communities, including flooding surfaces, surfaces of forced regression, subaerial unconformities, and condensed sections. In contrast, the subaerial unconformity is the only one of these that creates similarly abrupt transitions in nommarine systems.