This report describes the application of potentiometric multisensory system for estimation of water samples toxicity in terms of Microtox ® analyzer—a widespread instrument for toxicity evaluation. The working principle of Microtox ® analyser is based on a registration of luminescence from Vibrio fischeri bacteria. This luminescence depends on metabolism conditions and toxicity of the environment. Due to the fact that metabolism is influenced by multiple parameters the method is associated with certain limitations. Unlike this bioassay procedure the employment of multisensory system does not require the use of living organisms and can provide for faster toxicity evaluation. Fifty-five real and model polluted water samples, for which the toxicity was established by bioassay, were studied. The response of multisensory array processed with machine learning techniques allows for prediction of toxicity in terms of EC50 with relative errors of 20–25%. Taking into account the complexity of the task (simulation of complex biological reactions with inanimate instrument) this can be considered as a good promise for further research in this direction in order to develop instrumental alternative for toxicity assessment