While Sand Creek contains exotic trout species such as rainbow, brook, and brown, Medano Creek is an important habitat for native fish species. The Rio Grande Cutthroat Trout (Oncorhynchus clarki virginalis) historically occupied the Rio Grande Basin and associated drainages in southern Colorado and New Mexico. At present, it occupies about 15% of that range, mostly in the headwaters of the upper Rio Grande watershed. Medano Creek serves as an important biological refugia for this trout, because it is a closed system where exotic species cannot enter; the creek is bounded by an alpine basin at its source, and the Great Sand Dunes at its terminus.
Rio Grande Cutthroat Trout are catch and release only; they are on the candidate list for threatened/endangered species at the federal level. The US Fish and Wildlife Service determined in 2009 that while there is sufficient evidence to support federal listing, the listing is currently precluded due to higher priorities. These trout are currently on the Colorado state list as a Species of Special Concern.