A major aspect of biosedimentology focuses on biological processes that produce sedimentary structures and fabric. In marine environments this includes reefs as well as microbial structures and bioturbation. Mass extinctions exert a profound influence on these biosedimentological processes. That mass extinctions are defined by their effect upon metazoans implies they can have a strong affect upon reefs and bioturbation. The microbial record has been documented through the sedimentary structures which they produce, such as stromatolites in carbonates and wrinkle structures in siliciclastics. Marine environmental processes that cause mass extinctions and thus affect biosedimentology include changes in seawater temperature, carbonate chemistry and oxygen content. Changes in bioturbation due to mass extinctions are more likely caused by the negative affects of environmental changes that restrict bioturbators than extinction of bioturbators. Mass extinction processes that restrict bioturbators can affect development of the surface mixed layer and thus lead to changes in biogeochemical cycling. If there are changes in normal marine carbonate microbialites as well as siliciclastic wrinkle structures, then biosedimentological changes for a particular mass extinction are not just due to changes in ocean carbonate chemistry. Comparison can be made of changes in biosedimentology due to the end-Permian and end-Triassic mass extinctions, both caused by the environmental effects of large igneous provinces. Biosedimentological changes for microbial structures and bioturbation are more extensive after the end-Permian than the end-Triassic mass extinctions. However, recent work has demonstrated that the occurrence of microbial structures after the end-Triassic mass extinction is greater than previously understood. For both of these mass extinctions metazoan framework reefs were devastated, but the growing recognition of the presence of metazoans in Early Triassic microbial constructions has led to a more refined synthesis for this time. Continued work on understanding how these past episodes of environmental stress affected interacting biosedimentological processes that impact bioturbation, microbial structures, and reefs will help to manage for future environmental change.