Great Salt Lake hosts an ecosystem that is critical to migratory birds and international aquaculture, yet it is currently threatened by falling lake elevation and high lakewater salinity resulting from water diversions in the upstream watershed and the enduring megadrought in the western United States. Microbialite reefs underpin the ecosystem, hosting a surface microbial community that is estimated to contribute 30% of the lake’s primary productivity. We monitored exposure, desiccation, and bleaching over time in an area of microbialite reef. During this period, lake elevation fell by 1.8 m, and salinity increased from 11.0% to 19.5% in open-water portions of the outer reef, reaching halite saturation in hydrologically closed regions. When exposed, microbialite bleaching was rapid, driven by a decrease in surface chlorophyll. Bleached microbialites are not necessarily dead, however, with communities persisting beneath microbialite surfaces for several months of exposure and desiccation. However, superficial losses in the mat community resulted in enhanced microbialite weathering. In addition, we conducted microbialite community recovery experiments by incubating bleached microbialite pieces in lakewater and measuring changes in extractable pigments and DNA over time. We observed rapid recovery at salinities ≤ 17%, approaching 50% recovery within 40 days. 16S and 18S rRNA gene sequencing of extracted DNA indicated that recovery was driven by initial seeding from lakewater. At higher salinity levels, recovery occurred more slowly and may reflect accumulation and preservation of lake material in halite crusts vs. true recovery. Our results indicate that increased water input should be prioritized in order to return the lake to an elevation that submerges microbialite reefs and lowers salinity levels. Without quick action to reverse diversions in the watershed, loss of pelagic microbial community members due to sustained high salinity could prevent the recovery of the ecosystem-critical microbialite surface communities in Great Salt Lake.