The Doctoral Thesis has been prepared as a collection of thematically related scientific publications including five scientific publications. As a result of the research, a new method for assessing the toxicity of processing waters to the biocenosis of activated sludge has been developed. The most suitable microorganism cultures for increasing the treatment efficiency of active pharmaceutical ingredients and chemical oxygen demand by bioaugmentation have been selected in the screening tests. The possibilities and limitations of the reuse of processing waters in the pharmaceutical industry have been evaluated, and solutions for the reuse of chemically polluted waters in various stages of the processing water treatment process have been proposed.