From Pliocene to middle Pleistocene time, a large lake occupied most of the San Luis Valley above 2300 m elevation (7550 ft) in southern Colorado. This ancient lake accumulated sediments of the Alamosa Formation (Siebenthal, 1910), for which the lake is herein named. The existence of this lake was first postulated in 1822 and proven in 1910 from well logs. At its maximum extent of nearly 4000 km², it was one of the largest high-altitude lakes in North America, similar to but larger than Lake Texcoco in the Valley of Mexico. Lake Alamosa persisted for ~3 m.y., expanding and contracting and filling the valley with sediment until ca. 430 ka, when it overtopped a low sill and cut a deep gorge through Oligocene volcanic rocks in the San Luis Hills and drained to the south. As the lake drained, nearly 100 km³ (81 × 10⁶ acre-ft or more) of water coursed southward and flowed into the Rio Grande, entering at what is now the mouth of the Red River. The key to this new interpretation is the discovery of ancient shoreline deposits, including spits, barrier bars, and lagoon deposits nestled among bays and in backwater positions on the northern margin of the San Luis Hills, southeast of Alamosa, Colorado.

Alluvial and lacustrine sediment nearly filled the basin prior to the lake's overflow, which occurred ca. 430 ka as estimated from ³He surface-exposure ages of 431 ± 6 ka and 439 ± 6 ka on a shoreline basalt boulder, and from strongly developed relict calcic soils on barrier bars and spits at 2330–2340 m (7645–7676 ft), which is the lake's highest shoreline elevation. Overtopping of the lake's hydrologic sill was probably driven by high lake levels at the close of marine oxygen-isotope stage (OIS) 12 (452–427 ka), one of the most extensive middle Pleistocene glacial episodes on the North American continent. Hydrologic modeling of stream inflow during full-glacial-maximum conditions suggests that Lake Alamosa could fill at modern precipitation amounts if the mean annual temperature were just 5 °C (10 °F) cooler, or could fill at modern temperatures with 1.5 times current mean annual precipitation. Thus, during pluvial epochs the lake would rise to successively higher levels owing to sedimentation; finally during OIS 12, the lake overflowed and spilled to the south.

The integration of the upper (Colorado) and lower (New Mexico) reaches of the Rio Grande expanded the river's drainage basin by nearly 18,000 km² and added recharge areas in the high-altitude, glaciated San Juan Mountains, southern Sawatch Range, and northern Sangre de Cristo Mountains. This large increase in mountainous drainage influenced the river's dynamics downstream in New Mexico through down-cutting and lowering of water tables in the southern part of the San Luis Valley.