The evolution of human beings, along with the development of our increasing needs, started to shape the environment in order to adapt it to for every day requirements. Technological development and increasing demands for the satisfaction of our needs significantly affect the natural balance and threatens numerous ecological systems. However, it is possible nowadays to use scientific skills and knowledge in order to determine the threatening level of certain substance for the environment, as well as the living organisms. It is necessary to determine the environmental quality systems (SQS) for the protection of flora and fauna, as well as the maximal permissible concentrations (MPC) of particular substance in a certain media in order to protect human health, and environment in general. Pesticides, industrial chemicals, heavy metals, pharmaceutical compounds, personal hygiene products and by-products of combustion pertain to the group of priority substances. Environmental scientists and ecologists raised awareness of the presence and negative impacts of these priority substances. They also proved the importance of conscious handling, management and operation with these priority substances in order to minimize their discharge into the environment. Further considerations within this work will be directed toward regulatory standards of water contamination with priority substances and dangerously priority substances which have negative impacts on surface waters. There is also a list of 45 substances displayed as priority pollutants, which is provided by Water Framework Directive. In final segment of this work, the methods and possibilities for the detection of priority substances in aquatic environment are listed, along with the treatment options for the minimization of their negative impact in the environment.