Because of harbour security, ports often have areas of salt marsh, mangrove forest, wetlands, dune fields or other important intertidal or marine ecosystem, that are locally, regionally or even nationally important.
Each port will compile procedures and management plans for the management of the important natural ecosystems within its area of responsibility. These procedures and management plans will include the following, as appropriate:
- Ecological inventories of plants, animals, other biota and habitats, especially "Red Data" species and ecologically important natural systems such as fish spawning grounds or waterbird nesting areas
- Liaison with the local nature conservation authorities and local environmental interest groups
- Management actions required, e.g. fire management (burning programmes, firebreakers, culling, harvesting or restocking, monitoring, management of invasive alien biota)
- Opportunities for environmental education and appropriate environmental education programmes and facilities
- Prevention of encroachment by human activities, including illegal informal settlement, poaching, etc
- Features of archaeological or cultural importance, and their preservation
- A policy and procedure on angling and/or commercial fishing in the harbour, for instance a system of licenses with "no-go" areas demarcated to keep anglers away from the commercial areas
- Advising shipping, tenants and terminal operators of the protected areas
- Prohibition of hunting or disturbance of marine mammals in the port.