•Lyocell, polyester, and polypropylene microfibers found to be toxic.•Natural microfiber (lyocell) more toxic to D. magna than synthetics (PP and PET).•Toxic effects of microfibers (natural and synthetic) persist after exposure ceases.•Contrast in effects of microfiber exposure to food uptake and growth in D. magna.•Growth stunting and gut damage from natural and synthetic microfiber exposure. Microfibers, which are sourced from textiles and some products from the fishery industry, are the biggest contributors to microplastic pollution in aquatic ecosystems. In addition to these synthetic microfibers, naturally derived microfibers can also be found in aquatic environments. However, there are limited studies on the ecotoxicity of natural microfibers. To shed light on this topic, this study assessed and compared the toxicity of natural and synthetic microfibers on Daphnia magna, using lyocell, polyester (PET) and polypropylene (PP) microfibers. To evaluate the adverse effect of microfibers on D. magna, after effects including depuration, food intake, growth, mortality, and immobilization rate were continually observed for up to 96 h after the initial 48 h of exposure to the microfibers. Immobilization rate decreased in the following order: PP, PET, and lyocell. However, the depuration of microfibers in the lyocell and PET treatment groups was similar, with higher mortality rates than in the PP treatment group. Furthermore, despite the high rates of food intake following exposure, the lyocell and PET exposed groups exhibited growth inhibition during the same period. This growth inhibition corresponded with, and was likely due to, reductions in the length of gut microvilli, probably an expression of gut damage, which is believed to have reduced nutrient absorption in the affected individuals. Based on the results of this study, it was confirmed that even natural microfibers, and not just synthetic microfibers, can have adverse effects on aquatic organisms. This study confirmed not only the toxicity of microfibers, but also the consequences of their after effects. These results could be the basis for future research on the after effects of microplastics on aquatic organisms and provide directions for further microplastic ecotoxicity studies.