We compiled the global onshore-offshore distribution of marine bryozoans within 396 Permian–Early Jurassic bryozoan assemblages and show that bryozoan assemblage generic richness declined significantly in advance of the end-Permian and end-Triassic mass extinctions, starting as early as the Capitanian prior to the end-Permian and the Norian prior to the end-Triassic. We also show that offshore settings were affected first, prior to both extinctions, suggesting that environmental stress resulted from the gradual encroachment of some deep-water phenomenon onto the shelves. These patterns support long-term oceanographic, rather than extraterrestrial, extinction mechanisms, such as widespread euxinia triggered by massive volcanism and global warming. Tracking the onshore-offshore environmental distribution of these marine invertebrates provides a unique approach to assessing prolonged environmentally induced stress through this ∼120 m.y. time interval.