Abstract There were obtained water-soluble polyguanidines of various structures and molecular weights by polycondensation in the melt of aliphatic amines and guanidine hydrochloride in the presented report. There was assessed the toxicity of a number of polymeric compounds in the acute and chronic experiment on fish. In turn this allowed the visionof the link between the structure of the macromolecular chain and toxic action. There was established the average fatal concentration and the threshold level of the fatal effect, which does not exceed the range of 0.5-2.5 mg/l for different polymer structures. Taking into account the fact that such concentrations are destructive for many unicellular organisms, it is possible to predict their high efficiency in the fight against ectoparasites of fish.