Fossils of cutthroat trout have been found in deposits left by Lake Estancia; it appears to be the only fish species that lived in the lake. It appears to be most closely related either to cutthroat trout from the Pecos River east of the Estancia Valley or to an extinct middle Pleistocene trout from the San Luis Valley in Colorado. The fish was present in the lake during its freshwater stages, except very late during their history, when streams running from the Sandia and Manzano Mountains into Lake Estancia formed a favourable environment for spawning. Presumably, the trout entered Lake Estancia during its overflow phases and survived its lowstand phases in the lake's tributaries but were eventually wiped out during Holocene drought; no present-day reports of fish in the Estancia basin are known. Alternatively, the trout lived in former tributaries of the Estancia Valley that headed in the Sangre de Cristo Mountains but were later captured by the Rio Grande and Pecos River.