The upper Miocene to lower Pliocene Bouse Formation in the lower Colorado River trough of the American Southwest was deposited in three basins—from north to south, the Mohave, Havasu, and Blythe Basins—that were formed by extensional faulting in the early to middle Miocene. Fossils of marine, brackish, and freshwater organisms in the Bouse Formation have been interpreted to indicate an estuarine environment associated with early opening of the nearby Gulf of California. Regional uplift since 5 Ma is required to position the estuarine Bouse Formation at present elevations as high as 555 m, where greater uplift is required in the north. We present a compilation of Bouse Formation elevations that is consistent with Bouse deposition in lakes, with an abrupt 225 m northward increase in maximum Bouse elevations at Topock gorge north of Lake Havasu. Within Blythe and Havasu Basins, maximum Bouse elevations are 330 m above sea level in three widely spaced areas and reveal no evidence of regional tilting. To the north in Mohave Basin, numerous Bouse outcrops above 480 m elevation include three widely spaced sites where the Bouse Formation is exposed at 536–555 m. Numerical simulations of initial Colorado River inflow to a sequence of closed basins along the lower Colorado River corridor model a history of lake filling, spilling, evaporation and salt concentration, and outflow-channel incision. The simulations support the plausibility of evaporative concentration of Colorado River water to seawater-level salinities in Blythe Basin and indicate that such salinities could have remained stable for as long as 20–30 k.y. We infer that fossil marine organisms in the Bouse Formation, restricted to the southern (Blythe) basin, reflect colonization of a salty lake by a small number of species that were transported by birds.