Animal rearing has an impact on the natural environment, like all human activity. The major changes caused by aquaculture are related to the basic biological processes of living animals. Intensive farming of aquatic animals can modify the environment as a result of organic and inorganic nutrient loss, the discharge of veterinary products, genetic introgression, etc. The major causes of damage are associated with feeding and nutritional waste but appropriate methods to quantify the various forms of nutritional end-products are lacking. The major reported effect concerns the modifications affecting the benthos, the water quality and the fauna resulting from the build-up of organic matter. The adverse effects of dietary waste products can be avoided or reduced through improved nutrition, feeding management, water treatment and integrated aquaculture. This has encouraged the development of low pollution diets.