The main source of pharmaceuticals and their metabolites, but also drugs, viruses and pathogens are usually waste waters. Waste water treatment plants (WWTP) have a limited ability to remove these substances, which consequently leads to their appearance in the environment. This review describes the reasons of WWTP's limited effectiveness, behaviour of pharmaceuticals and drugs in WWTP and also summarizes alternative biological, chemical and physico-chemical procedures and their modifications, able to effectively clean and disinfect waste waters. The paper also focuses on the virus issues which often occur in waste water, and describes how to eliminate them. Within the scientific community, the SARS-CoV-2 virus is currently being intensively studied due to the ongoing pandemic but the behaviour of the viruses and their inactivation in waste waters is still examined inadequately.