Lake Abert, a terminal alkaline salt lake in south central Oregon, has been a key staging area for migratory waterbirds along the Pacific Flyway. In 2014, the lake shrank to about 5% of its maximum size, and its salinity increased from 75 g • L^-1 to 250 g • L^-1. This resulted in a major ecosystem shift from one dominated at higher trophic levels by invertebrates and waterbirds to one composed primarily of hypersaline-adapted microbes. A large variety of halophilic bacteria and archaea were also detected using 16S rRNA metagenomic sequence analysis. The loss of prey and staging habitat for migratory waterbirds was especially pronounced for Eared Grebe, Red-necked Phalarope, and Wilson's Phalarope, all of which feed on brine shrimp and alkali flies. The last time the lake was in this state was nearly a century ago during the Dust Bowl of the 1930s, which was a once-in-500-years drought. To understand the causes of the current event, we examined hydrological, climatic, and biological data. The primary cause of the event appears to have been the combined effects of upstream water diversions and lower river flows that were exacerbated by a moderate decade-long drought and elevated evaporation rates.