Microplastics are now widespread throughout the environment, but there is still scarce knowledge about their impact on freshwater invertebrates, especially from tropical environments. In this study, we carried out experiments to investigate the harmful effects of polyethylene microplastics (MPs 40–48 µm in size) on Chironomus sancticaroli and Daphnia magna, which are bioindicators from different climate zones. In short-term exposures, the MPs presented no significant effect on the survival and mobility of the species, although D. magna showed 51 ± 10% of the intestinal tube filled by MPs after 96 h of exposure to 320 mg MP L−1. Chronic exposures showed that C. sancticaroli has its larval length reduced in the 320 mg MP L−1 treatment (p ≤ 0.05), presenting EC10 of 302.36 mg MP L−1 for larval growth. Similarly, D. magna had its body length reduced after 21 days of exposure to 160 and 320 mg MP L−1 treatments (p ≤ 0.05). On the other hand, the dynamics of the molting cycle was not affected by the MPs in chronic exposures. Our findings support the recent discussion regarding the variable and complex effects of microplastics on the biota, which depend on the model species and exposure time, showing that species growth can be potentially impacted by microplastic pollution. The prediction of this biological endpoint in organisms representing tropical and temperate environments indicates a warning of the potential harm of the microplastic presence in continental waters.