The invasive diatom Didymosphenia geminata (Lyngbye) Schmidt, D. geminata has invaded the austral zone of Chile, causing significant ecological, scientific and societal concerns. We aimed to evaluate the viability and motility Daphnia magna (D. magna), as a biosensor for effects of D. geminata. Toxicity assays were performed in dilutions of river water alone (V/V dilution) and in river water contaminated with D. geminata (V/V dilution) or polyphenols extracted from D. geminata under controlled conditions and different time (acute 30 min and 7 hrs). Our results indicated that D. magna was sensitive to increasing concentrations of D. geminata extracts. We observed a 50% (IC50) viability reduction after 24 h of exposure to a 0.023 V/V dilution and the same value when using polyphenols from D. geminata; additionally, this treatment further reduced the motility capacity by 50% after 72 h. The D. magna organisms were acutely responsive, showing a 50% reduction in frequency at 15 min. We conclude that D. magna is sensitive to polyphenols produced by D. geminata in rivers, suggesting potential chronic toxic consequences on several aquatic species following exposure to these diatom substances.