The study evaluated the effects of benzalkonium chloride (BAC) and atrazine on the macrophyte Elodea canadensis (Michaux) using a miniaturised monitoring test system consisting of a microbioreactor of reduced volume and integrated sensors for the online measurement of physiologic parameters, like oxygen production and different parameters of fluorescence. Different concentrations of both chemicals were applied to leaves of E. canadensis and the physiologic endpoints evaluated after 1h. A concentration-dependent reduction of the oxygen production and of the effective quantum yield of energy conversion was recorded. The mini-PAM technique implemented in the presented system allowed for a clear monitoring of the kinetic of BAC and atrazine, showing their distinct mode of action. No observable adverse effects were recorded up to concentrations of 2.5 mg/L and 10 microg/L, for BAC and atrazine, respectively. These values are in accordance with available results in the literature, hence indicating that the microbioreactor test system might be suitable, on the one hand, for the laboratory screening of potential short-term toxicity of contaminants on aquatic plants, and on the other hand, serve as an in situ field biomonitoring system for the rapid detection of pollutants in water.