Anthropogenic pressures on freshwater ecosystems are growing and pose serious threats to endemic fish species. This study aimed to identify the effects of anthropogenic pressures on an endangered species, Pseudophoxinus crassus (Ladiges, 1960), in the semi-arid Konya Closed Basin of Türkiye. The distribution area of the species was found to be reduced and the only population sampled exhibited a high incidence of external anomalies. It is hard to identify the origin of the anomalies; however, abrupt increases in salinity and reductions in dissolved oxygen values indicate that intensive agricultural activities might be responsible for the pressures on the population. Additionally, temporal changes in population growth parameters were identified and the effects of anomalies on fish condition factors were examined. Fulton’s condition factor was found to be reduced among specimens with external anomalies. This relationship between anomalies and fitness as reflected by the condition factor was also observed for two other endemic species. It is unclear whether these anomalies affect feeding behaviours, although specimens with lower condition factors are more likely to exhibit anomalies. However, it is clear that without the rehabilitation or restoration of natural habitats, fitness reduction will severely affect the statuses of populations, particularly in cases of isolated populations.