Gilbert’s reports on Lake Bonneville are, like his Henry Mountains report, classic contributions to geology, but the two studies are very different. The Henry Mountains study involved only 2 months of field work, and the report was completed and published within months after completion of the field work. The Lake Bonneville reports were based on many seasons of field work, first with the Wheeler Survey, then the Powell Survey, and finally the U.S. Geological Survey. Writing and publishing his final report on Lake Bonneville were delayed.

He recognized three main stages of the Pleistocene lake: (1) an early stage represented by what is now known as the Alpine Formation, a major interruption in lake history represented by an unconformity between the early and late lake deposits; (2) another rise of the lake to its highest level, the Bonneville shoreline, overflow of the lake into the Snake River via a gap at Red Rock Pass; (3) drop of water level about 300 ft as the outlet was eroded downward to a bedrock lip, and stillstand of the water at that level (Provo stage) to produce what is known as the Provo Formation. The lake history ended with another 300-ft drop to a poorly developed shoreline (Stansbury stage). The subsequent drop in level of about 300 ft to the level of the Great Salt Lake probably should be considered post-Bonneville history, although Gilbert was vague about the terminal stage.

Gilbert clearly recognized that the lake basin and its islands and peninsular mountains were formed by Tertiary diastrophism. Pre-Bonneville erosion of the mountains produced huge alluvial cones around the mountain bases and partly filled the basins. Lake Bonneville was formed after the alluvial cones and after most of the faulting and volcanism. Faulting, volcanism, and deposition of alluvial cones were renewed during and since the formation of the lake.

Two major contributions to structural geology include recognition of repeated displacements on faults along the Wasatch Front and doming of the lake basin as a result of isostatic rise due to unloading of the crust as the lake desiccated. Both structural contributions have been amply confirmed by modern surveys.