In the agricultural sector, the introduction of organic compounds into water systems poses a threat to aquatic organisms. Due to the increasing use of natural chemicals in our daily lives, there exists the possibility that water resources will continue to be contaminated. The introduction of these micropollutants into the hydrological cycle is examined from both nonpoint sources and points of discharge. The sources of particular classes of natural chemical micropollutants from commercial and domestic sources are analyzed. Several nonpoint-source transport channels are thought to be responsible for the introduction of organic pollutants into the world's seas. These include atmospheric deposition, direct runoff from coastal communities, and indirect runoff from agricultural areas via rivers and streams. Rivers also play a role in the transport of biodegradable waste products from upland surface waters (where they are dumped via industrial and municipal effluents) to the seas. Most municipal and industrial wastewater contains a large amount of a wide variety of organic compounds. This is thus a significant source of pollution of aquatic environments with these organic compounds. As a result, what is critical is the search for methods that can effectively treat wastewater, as well as other polluted water. This is an imperative part of protecting the natural environment. The increased use of chemicals in everyday life, together with unrestricted access to medicines, has increased waste production, as well as an ensuing influx of both common and new organic compounds into the environment. In recent years, new organic compounds have become more and more evident in environmental samples, called emerging organic contaminants (EOCs). Various pollutants can have different effects on the aquatic environment. Even though many pollutants (e.g., organic materials, N and P) may be beneficial in low concentrations, at high concentrations they can adversely affect the ecological balance of the system. Physical pollution of a river system can have a wide variety of effects on the ecology of the system, including altering the feeding and breeding habits of different species. In addition, some biological pollutants in water can spread diseases throughout the ecosystem, as well as disrupt it.