The objective of the study was to investigate pollution sources in the Vilnia River and evaluate the toxicity of sewage, contamination of the Vilnia River water and bottom sediments, using a complex of biological methods. Toxicity was assessed by use of various indices of test-organisms: seed germination and root growth in Lepidium sativum L., and mortality and physiological indices in early ontogenesis (embryos and larvae) of Oncorhynchus mykiss L. Changes in biological indices of Lepidium sativum L. and embryos and larvae of Oncorhynchus mykiss demonstrated that sewage of an identified point of the pollution source and the water of the Vilnia River 300 m downstream from the pollution source, bottom sediments of the Vilnia River nearby the pollution source and 300 m downstream from the pollution source could be defined as toxic.