Cutthroat trout (Oncorhynchus clarki) fossils in the Quaternary-age lacustrine sediment of the Estancia Valley provide insight into the paleolimnologic history of the valley. The presence of fish is evidence that a pluvial system overflowed into the Pecos River watershed. Most likely, the overflow occurred during the expansion of Early Lake Estancia, an Illinoian or pre-Illinoian pluvial lake known only in subcrop. Once established in the Estancia watershed, trout occupied headwater streams and only intermittently migrated and resided in developing lake systems. The headwater streams served as refugia through the Sangamon(?) and early and middle Wisconsin time when a fresh-water lake did not exist in the valley. With the advent of full-pluvial conditions during the late Wisconsin, trout migrated from headwater streams into the first of three fresh-water phases of Late Lake Estancia. On two occasions, climate shifted to warmer and drier conditions, causing significant lake-level drawdown. Salinity increased and trout were eliminated from the lake, only to be reintroduced during the next fresh-water phase. Near the close of the late Wisconsin, Late Lake Estancia waned and desiccated, but headwater streams remained as fish refugia. Following the interpluvial episode, the basin again filled, culminating in Lake Willard, considered to be of latest Wisconsin age. With evolution into a fresh-water body, trout migrated into a lake environment for the last time. Ensuing hot/dry conditions brought about the desiccation of Lake Willard and severely impacted the headwater streams. This factor, in possible combination with human fishing activity, led to the elimination of fish from the Estancia Valley after a continuous occupation of at least 130,000 yr.