USFWS (2010) summarized threats as follows:
The primary threats are: (1) habitat loss from the potential loss of spring flow due to a decline in groundwater levels, and (2) hybridization or competition with Western Mosquitofish initially due to the local habitat modifications, but now caused by the failure of the upper dam to maintain a barrier between spring outflow and downstream habitats. Available information does not indicate that impacts to spring flows from significant increase in groundwater use or declines in recharge is imminent (defined as likely to occur in the next 10 years) at this time. However, it is likely to occur over the foreseeable future of 50 to 100 years as a result of climate change and the increasing human need for more water resources. The magnitude of impact on the Clear Creek Gambusia if this threat were realized is extremely high. Because the range of the species is limited to one small, isolated location, habitat modification due to a decline in spring flows could result in its extinction. The threats associated with hybridization and competition may be occurring now due to the recent erosion of the upper dam allowing renewed access to the upper spring pool by Western Mosquitofish. If the impacts of these threats are the same as observed in the past between 1953 and 1978, then the population of Clear Creek Gambusia will be depressed, but not eradicated until the upper dam can be repaired. Therefore, the magnitude of the impact of this threat on the species is considered moderate to high. Secondary threats include habitat modification from water quality degradation, local habitat changes, lack of regulatory mechanisms, and introduction of a disease, parasite, or nonnative species (resulting in competition or predation). None of these concerns acting alone result in substantial threats to the species, but together any of these could negatively impact the Clear Creek Gambusia. Climate change is another source of potential threats to the species. All possible impacts associated with future climate change cannot presently be reliably predicted. However, accelerating climate change will exacerbate any of the threats already considered or could result in whole new threats that are not conceived at this time. Either way, subtle but significant changes in the ecosystem of the Clear Creek Gambusia resulting from climate change in the foreseeable future of 50 to 100 years could cause the species extinction and is a threat of high magnitude. All of these threats, both primary and secondary, must be considered in the context of a fish with an extremely small range with no opportunity for movement, a relatively small population size, and a very short life span. Because of these factors, the magnitude of impact of any potential threat or future stochastic event is exceptionally high. Any events negatively affecting the species or its habitat could result in complete extinction of the Clear Creek Gambusia.