The fecundity and sexual structure of weatherfish (Misgurnus fossilis) population, an inperilled and protected freshwater fish with a poorly known life history, was studied in three waterbodies: the River Ner, the Południowy canal and the Nowy Rów canal (Poland) differing in hydrological character. We compared reproductive traits; i.e. sex ratio, absolute and relative fecundity, oocyte size, gonado-somatic index and body condition. In all study sites, the sex ratio of weatherfish did not differ from parity (1: 1), though in the River Ner, the highest GSI values were recorded for females whilst male GSI did not differ among sites. The absolute (FA = 2860 ± 2065) and relative fecundity (FR = 120 ± 55 eggs per g of female body weight) in the River Ner were significantly lower than in the other two sites. In the River Ner the frequency distribution of oocyte diameter, decomposed using the Bhattacharya method, showed two distinct groups in equal numbers. Oocytes that were ready to spawn were larger in the River Ner than in the Południowy and Nowy Rów canals. Fish in the River Ner were also characterized by the lowest Fulton condition index (mean K = 0.36 ± 0.1). The trade-off between impaired fecundity and increased egg diameter may result from the different nature of the studied watercourses or levels of endocrine-disrupting chemicals (EDCs), such as steroid compounds.