In this study we tested the effects of a neurotoxic strain of the cyanobacterium Raphidiopsis raciborskii (CYRF-01) on the swimming activity and physiological parameters of Daphnia similis such as movements of the antennae, thoracic limbs, post-abdominal claw and heart rate. An acute assay was performed to test the effect on swimming activity, exposing newborns (b24 h) to different concentrations of live cells and observing the number of immobilized animals over a period of 48 h. For testing the effects on physiological parameters adult females (10–15 days) were exposed in a flow-through system and recorded with a digital camera. Results showed rapid effect of the strain CYRF on all parameters. Animals started to be immobilized in the first 30 min exposure and showed complete paralysis after 2 h in 500 μg L−1 and after 24 h in the other concentrations. Physiological parameters accompanied the same response pattern with effects starting after 30 min and some recovery at the end of 6 h exposure. Antennae stopped moving after 2–3 h at 250–500 μg L−1, explaining the paralysis of the swimming activity in Daphnia. Thoracic limbs movements were significantly inhibited after 30 min in all concentrations, staying at lower levels than control through the experiment. Post-abdominal claw movement were completely ceased after 30 min and remained stopped until the end of the trial. Heart rate showed a tendency to decrease abruptly in the first 30 min exposure in all concentrations, but showed significant lower values than control only at 500 μg L−1, between 3 and 4 h exposure, and a recovery at the end of 6 h. In conclusion, results show that neurotoxic cyanobacteria can impose severe constrains on the physiology of daphniids, which can have consequences to the oxygen uptake, swimming and feeding behavior and to the overall fitness of those organisms.