Goodeinae is a subfamily of critically endangered fish native to central Mexico. Populations of Skiffia lermae, a species belonging to this subfamily, have significantly decreased in the past two decades. A previous study showed that S. lermae is sensitive to acute nitrate-nitrogen (NO3-N) exposure, leading to noticeable changes in both behavioral and histopathological bioindicators. The aim herein was to determine the vulnerability of S. lermae to NO3-N exposure at realistic concentrations registered in freshwater ecosystems in central Mexico where the species was historically reported. Offspring of S. lermae were chronically exposed during 60 days to concentrations of 5, 10 and 20 mg NO3-N/L, with 2 mg NO3-N/L used as the reference value (control). Survival rate, feeding behavior, aquatic surface respiration, body growth, scaled mass index, immature red blood cells, as well as histopathological changes in branchial, hepatic and gonadal tissues were evaluated. Additionally, this study analyzed water quality in freshwater ecosystems where S. lermae presently persists. The results showed decreased survival as NO3-N concentration increased, as well as increased feeding latency, aquatic surface respiration and histological damage in the gills and liver. These organs showed differential sex-dependent responses to NO3-N exposure; females were more sensitive than males. In the ovaries, a decreased density of stage III oocytes was associated with increased NO3-N concentrations. No changes were observed in body growth and number of immature red blood cells. Concentrations recorded in the three freshwater ecosystems that S. lermae inhabit were below 2 mg NO3-N/L. Together, the results could explain why the species has disappeared from more contaminated freshwater ecosystems where NO3-N levels exceed 5 mg/L. Moreover, the study warns about the risks of increasing NO3-N concentrations in the current sites where the species lives.