Identification of contaminants, determination of their biological hazard and content in water are important practical tasks while assessing water quality in sources of drinking water supply of large cities. Presented herein is a review regarding pharmaceutical pollution of waters in various countries. Given are original data concerning contamination of water objects—sources of water supply of Moscow with components of pharmaceuticals and metabolites of therapeutic agents. Worked out is a retrieval and calculation technology of assessing hazards of substances. Proposed is the use of “structure-activity” calculation technologies for prediction of side effects of pharmaceuticals and pharmacological activity of other organic xenobiotics not used in medicine. Certain ways of decreasing pharmaceutical pollution are recommended.