Nearly all inland water bodies have been modified to some extent through human intervention. For instance, the enriching effects of excess fertilizers and livestock wastes in the runoff from farmland and lakes have caused biological environmental impacts on rivers and streams.

New ecosystems have been created by the physical modification of natural aquatic ecosystems, such as rivers and streams that have been dammed to form reservoirs and irrigation systems for agriculture.

Reservoirs themselves can be engineered in special ways to facilitate, for example, fish passage and fish capture or otherwise to stimulate increased production through habitat enhancement for a specific species. Natural and modified ecosystems are further transformed in their particular community structures through biodiversity - by the introduction of new species - and by periodic stocking.

All modifications affect the fisheries potential of aquatic ecosystems. Many are subtle, with long-term irreversible effects and may eventually prove negative, but are not easily perceived as such at the time they are implemented or occur.

Large reservoirs are among the most conspicuous man-made aquatic ecosystems. Many small water bodies seem natural but, in fact, are reservoirs that have been created primarily as community water supplies, to water livestock or to irrigate crops. Such water bodies can have multiple uses, including fisheries and aquaculture but, to be successful, they require well-planned integrated watershed management. Rice paddies are a prime example of an agricultural crop system that produces a second crop - fish - which in turn enhances the rice production.