The majority of reports on the toxic effect of cyanobacterial metabolites on the freshwater invertebrates is based on determination of two endpoints: mortality or immobilization. However, detection of sub-lethal effects requires more sensitive indicators The aim of the present study was to evaluate the applicability of digital-video analysis for determination of early behavioral and physiological responses in the assessment of effects caused by the cyanobacterial neurotoxin, anatoxin-a (ANTX) at a broad range of its concentration (0.5–50 μg/mL). Swimming speed (SS), heart rate (HR), oxygen consumption (OC), thoracic limb activity (TLA) and abdominal claw movement (ACM) of Daphnia magna were evaluated. Swimming speed and abdominal claw movements were determined by digital analysis of video clips by Tracker® software; OC by Oxygraph Plus System® while HR, TLA and ACM by digital frame-by-frame analysis of video clips of microscopic view with the use of a media player software. The experimental study showed a concentration- and time-dependent decrease of SS, HR, OC, TLA and ACM. SS was inhibited as early as after 10 s of the exposure of Daphnia magna to ANTX, and the other physiological responses after 2 h. Further inhibition of these parameters was also noted after 24 h of the exposure. On the other hand, stimulation of ACM was noted at the lower (0.5 and 2.5 μg/mL) ANTX concentrations after both 2 h and 24 h of exposure. The results indicated that some behavioral and physiological biomarkers measured by video analysis may be a valuable tool for an early determination of toxic effects induced by cyanobacterial metabolites in zooplankters.