Stalked crinoids were common in shallow-marine habitats in the geologic past but are today restricted to the deep sea. The timing of the shift in their bathymetric distribution has been discussed in the context of the Mesozoic Marine Revolution (MMR), one of the most important episodes of change in marine ecosystems of the Phanerozoic, which is generally thought to have begun sometime in the Late Triassic. However, the record of Cretaceous stalked crinoids is poor, consisting primarily of disarticulated ossicles for which the provenance is often difficult to determine, hampering interpretations of the habitat in which they lived. Here, we report on well-preserved isocrinids from the Aptian and use a multidisciplinary approach involving sedimentological, isotopic, and paleontological data to demonstrate that they inhabited a shallow lagoon subject to salinity variations. This suggests that their absence from such environments today is not a function of physicochemical factors and reinforces the idea that predation pressure may have played a critical role in their bathymetric distribution. The influence of predation is supported by the first Early Cretaceous record of a regenerating arm.