A chronological relationship between the annual profiles of stress hormone cortisol and male (testosterone and 11-keto testosterone) and female (17β-estradiol) sex steroids, the key regulator of annual reproductive cycle has been sought in two different group of fish (Mystus gulio and Parambassis ranga) under natural photothermal conditions. The serum samples were collected at two different times in each month (from January to December) and the same was repeated for two consecutive years throughout an annual cycle. The fluctuations of major physical factors (temperature, salinity, pH, dissolved oxygen and carbon dioxide) and presence of three important heavy metals were also estimated accordingly. Therefore, the present study aims to explore the rhythmic responses of sex steroids and cortisol to assess the impact of different environmental stressors on selected fish species. We tried to develop a realistic conceptual idea to analyze and predict the effect of changing environmental parameters on the possible shift in the rhythmicity of aforesaid hormones in two different groups of fish and their adaptive responses to thrive in such environment. Our results indicated that the fluctuation of circannual rhythms of testosterone, 17-β estradiol and 11-KT varied according to species, was related with the physical factors of the aquatic system and temperature was the most important factor among them. This information might help to frame the reproductive strategies for different fish species, as well. © 2017 Informa UK Limited, trading as Taylor & Francis Group.