Environmental management systems are also starting to evolve for some forms of aquaculture, as well as more formal environmental management systems (EMS). EMS is a complex approach with little direct application to small- and medium-sized farms, however, EMS principles provide useful guidance for improving environmental management of aquaculture production systems.
EMS assemble management policies, programmes and practices designed to identify links between industry, urban and developmental activities, and consequent pressures on the environment. An effective EMS for aquaculture should establish indicators of changes in the environment, including land, water and aquatic resources. Policies and practices responding to the changes are implemented with continuous feedback to reduce/mitigate any environmental impacts. These indicators should make clear links between environmental impacts and aquaculture activities. The indicators should also reflect positive and negative impacts of environmental influences on aquaculture, as well as visa versa.

