Explorers as early as Captain J.C. Frémont in 1843 recognized shoreline evidence that a succession of deep lakes had once existed in the Great Salt Lake basin. However, G.K. Gilbert, first with the Wheeler Survey in the 1870s and later with the U.S. Geological Survey, was the first to study these prehistoric lake features and describe the major features of Lake Bonneville. He named the lake after Captain Bonneville, an earlier explorer in the region to the north, but one who never visited Great Salt Lake.

Gilbert established that the lake, with a maximum depth of at least 1,000 feet, covered an area of about 20,000 square miles in what is now northwestern Utah, northeastern Nevada, and southeastern Idaho. He determined that at its highest level, which he named the Bonneville Shoreline, Lake Bonneville overflowed the rim of the Great Basin near Red Rock Pass in southeastern Idaho at an elevation of about 5,100 feet above sea level and spilled into a tributary of the Snake River, eventually flowing into the Pacific Ocean. He concluded that when these waters suddenly breached the relatively unconsolidated sediments forming the pass, they quickly scoured a channel down to the bedrock and released a catastrophic flood down the Snake River. This event, now known as the Bonneville Flood, lowered the outlet elevation and reduced the surface elevation of Lake Bonneville in a short time, probably less than a year, to a more stable level at about 4,750 feet above sea level. Gilbert named this post-flood level the Provo Shoreline.