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Cyanobacterial blooms affect aquatic ecosystems due to their capability of producing cyanotoxins (e.g., microcystins, MC; cylindrospermopsin, CYN) and other bioactive compounds. Filter feeding zooplankton are amongst the first organisms affected and research has mainly focused on their interactions with toxic cyanobacteria. We investigated oxidative stress, biotransformation and energetic responses of Daphnia magna after exposure to cyanobacterial extracts and behavioral changes of the animals exposed to living cells of non‐MC and non‐CYN producing strains. Enzyme and energetic responses were measured in time kinetic experiments, using extracts of Microcystis botrys, M. wesenbergii, Aphanizomenon aphanizomenoides, Cylindrospermopsis raciborskii, corresponding to 10 mg DW L−1. In behavioral experiments, D. magna was exposed to living cells of Microcystis aeruginosa, A. aphanizomenoides, Dolichospermum circinalis, C. raciborskii, at the density of 400 000 cells mL−1 using a Daphnia toximeter equipment. Despite not producing MC or CYN, some cyanobacterial extracts caused significant increase of biotransformation enzyme, especially catalase, activities from the exposed D. magna after a longer incubation. Total carbohydrates and glycogen contents were increased but the activity of one of the involved enzymes, the malate dehydrogenase, was not changed. Animals' behavior (e.g., swimming, position within water column) was altered in exposures to cultures of C. raciborskii and D. circinalis. These physiological and behavioral alterations indicate stress, which may impair overall performance of zooplankton at the environmental realistic chronic exposure scenario.