In the last few decades growing attention has been paid to the occurrence and impact of micro-pollutants such as pharmaceuticals, personal care products, surfactants and other industrial additives on aquatic ecosystems. The effect on Daphnia magna of two pharmaceuticals (Na-diclofenac and paracetamol), a hormone (17β-estradiol), a personal care product additive (triclosan), a psychoactive drug (nicotine) and of a pesticide (metazachlor) was determined at different concentrations (0.01–10,000 μg/L) during 24 and 48 h exposure. In order to test the sensitivity of this innovative heartbeat rate test the results were compared to those of the immobility and lethality tests, traditionally applied to Daphnia. The heartbeat rate as a toxicity endpoint for metazachlor, Na-diclofenac, ß-estradiol and triclosane as well as for paracetamol showed significantly higher sensitivity than the immobility and lethality; the lowest observed effect concentrations were 0.05, 0.1, 0.1, 0.5 and 500 μg/L, respectively. Our study provides the evidence that the heartbeat rate of water flea is a more sensitive and ecologically more relevant endpoint than the conventionally applied immobilization and may become a novel model system for studying the effects of micro-pollutants on freshwater ecosystems.