Selenium (Se) is an essential yet potentially toxic element in aquatic ecosystems that undergoes transformation from inorganic to organic forms. However, the bioaccumulation and toxicity of different Se species across aquatic food chains remain poorly understood. In this study, three microalgae species were exposed to selenite (Se(IV)) or seleno-L-methionine (Se-Met) (0-1000 μg/L) for 120 h, followed by dietary exposure of Daphnia magna to Se-contaminated C. pyrenoidosa (1-50 μg/L). The results showed that the 96 h EC50 of the 3 algae to the two Se species differ, with C. pyrenoidosa the most resistant and S. capricornutum the most sensitive. In addition, the toxicity of Se(IV) is significantly higher than that of Se-Met in 2 of the 3 algae. However, the growth and antioxidants biomarkers of the 3 algae after Se exposures are more affected by algal species rather than Se species. For the bioaccumulation and trophic transfer of Se in the algae and D. magna, we found higher bioaccumulation of Se-Met in algae than Se(IV). But Se bioaccumulation in the D. magna via dietary exposure was not affected by Se species. In D. magna, Se-Met is more toxic than inorganic selenium Se(IV). Moreover, Se-Met caused a 66% reduction in cumulative offspring production relative to Se(IV) treatment. This study provides a foundation for investigating Se trophic transfer mechanisms in freshwater food webs.