Alterations to natural habitats are becoming more common due to changes in anthropogenic land use. As such, there is increasing interest in determining how wild animals adapt and respond to environmental stressors. The glucocorticoid (GC) stress response enables animals to react appropriately to environmental challenges but can be affected by many factors, two of which are habitat quality and time of year (i.e., season). This study tested whether baseline and maximum (stress-induced) whole-body cortisol concentrations varied in relation to habitat quality and season using wild central mudminnows (Umbra limi) collected from two connected streams differing in habitat quality in each of four seasons. Overall, baseline and maximum cortisol levels did not differ significantly between the two systems but there was evidence of a seasonal effect. Baseline cortisol levels in the fall and summer were significantly (P<0.01) lower than those in winter and spring and maximum cortisol levels in the summer were significantly lower (P<0.01) than those in the spring. Inconsistent with the prevailing paradigm, our results indicate that habitat quality does not always influence baseline GCs or the stress response. In contrast, baseline and maximum GCs in this species do vary seasonally. As such, seasonality should be considered in the interpretation of stress response data especially when using small-bodied stream fish as biological indicators.