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The extreme seasonal environmental variation of intermittent rivers has a profound effect on freshwater fish communities. Yet, few studies have examined the consequences of the seasonal cycles of flooding and drying to fish condition and reproduction in these ecosystems. In this study, we compared the body condition, reproduction and diet of two chub populations from two adjacent sites (a perennial and an intermittent site) on the main stem of a Mediterranean river (Evrotas River, S. Greece). The study was conducted in spring 2017, three months after flow resumption and before the onset of chub reproductive period. Condition (net weight adjusted for length) of fish did not differ significantly between the two sites, despite lower aquatic macroinvertebrate availability at the intermittent site. Fish at the intermittent site compensated for the lower aquatic prey availability by increasing their feeding intensity and by shifting to higher terrestrial prey consumption. In addition, chub liver weight (adjusted for length) and gonadal weight (adjusted for length) were significantly higher at the intermittent site, indicating higher somatic and reproductive investment. These results highlight the resilience of fish populations inhabiting streams with extreme variation in flow, due to natural and/or anthropogenic drought.