Habitat Impacts

Fish Aquaculture @TNC

Nearshore marine environments are often characterized by sensitive and key habitats such as mangroves, nursery and spawning grounds, seagrass beds, and migratory routes. If fish cages are not sited properly and correct managerial protocols are not strictly followed, long-term cage operations can cause detrimental impacts to the seafloor and to critically valuable environments.

Some of these negative effects on the environment caused by poorly sited and managed cages is reduction of abundance and diversity of local benthic species and habitats that are essential to the ecosystem, increase in dissolved organic solids and nutrients that the environment cannot sequester, decrease of water quality below safe levels, and impacts to sensitive ecosystems surrounding the cages. If permitters and managers follow strict siting protocols while taking into account numerous environmental factors, coastal finfish cages can have minimal impact on the environment.

impact mitigation of aquaculture

Impact mitigation of aquaculture. When properly sited, fish farms can have a minimal effect on surrounding habitats and water quality. Source: opens in a new windowScite Science Communication

Site Selection

An incredibly important issue to consider when planning or permitting finfish aquaculture cages in tropical reef areas is the distance from coral reefs. Coral reefs are sensitive ecosystems that provide shelter and nursery grounds to many reef fish and can be negatively affected by slight changes in water quality from nearby finfish cages. Natural fish waste from a cage will slowly fall to the seafloor, which can build up on the seafloor if the cage is too shallow or if there is low flow. However, if good currents exist, waste can instead be transported downstream and dissipated in the environment; if ingoing and outgoing tides also exist, then waste can be transported and dispersed in both directions. ref

Similar to coral reefs, seagrass beds and other sensitive habitats (spawning grounds and nurseries) need to be considered during the planning and permitting phase. Seagrass beds provide food for marine mammals such as dugongs and habitat for fish, but fish waste or excess feed from cages can cover seagrass beds, blocking out light needed for photosynthesis. Horizontal distance as well as currents and tides need to be taken into account to safeguard the preservation of these sensitive habitats. ref

Depending on a variety of environmental parameters, species selection, and regulatory and permitting frameworks, the allowed distance of finfish cages to sensitive habitats can vary greatly, which makes it difficult to set a concrete and universal minimum distance. Here are a few examples to demonstrate how distance recommendation may differ depending on the country of origin, habitat to be protected, or by what organization or body is proposing such recommendation.

LocationEnvironmental ParameterRecommended DistanceRecommending Body
Gulf of Mexico, USABenthic communities152 mFederal Agency (BOEM)
California, USAEelgrass beds10 mFederal (NOAA) & State Agencies (CCC)
PalauCoral reefs200 m (siting guideline)Local government & NGO

Source: Recommended Distance – United States Department of the Interior (Gulf of Mexico, USA), State of California Natural Resources Agency (California, USA), Hedberg et al. 2015 (Central Vietnam and Palau)


Waste generated from a cage can be properly and naturally sequestered and utilized by the marine environment if there is proper current and the ecological limits of the environment are not exceeded. If excess nutrients are produced from the cage during feeding and the waste cannot be assimilated, they can build up and cause long-term damage to the local area. If excess feed and feces accumulate on the surrounding seafloor, increased respiration from microbial decomposition will lead to the depletion of oxygen in the sediment and alter its chemistry. As oxygen is depleted by microbial respiration, anaerobic bacteria will begin to prevail leading to hypoxic or anoxic conditions and to the production of carbon dioxide, nitrification of ammonia, and the reduction of manganese, iron and sulfur.

If the seafloor is allowed to shift towards an anaerobic bacterial community, mats of sulfide oxide will colonize the affected surface and will be the only visible organism. Seafloors beneath finfish cages that have undergone alteration in physical and chemical alteration have also seen changes in species composition and diversity. Studies have found that there is a shift towards more tolerant generalist organisms such as polychaetes, and a decrease in mollusks and crustaceans. ref

If proper planning and management are carried out while taking into account currents, tides, and the proper feeding protocols, it is possible to minimize negative impacts to the surrounding environment. ref


  • Avoid disruption to native biodiversity, especially protected species
  • Site farms away from corals, seagrass, mangroves, and other sensitive habitats, and make sure that gear and moorings are not damaging habitats
  • Employ methods to minimize physical disturbance to habitat, including but not limited to ensuring appropriate depth and current for cages
  • Implement cage rotation or fallowing if nutrient loading exceeds the ecological threshold
  • A generally accepted distance from corals is 200 meters to have minimal impacts on water quality, benthic environment, and sensitive habitats


Seafloor Depth

Depending on the speed of the currents in the proposed or current cage site, greater depths may be needed to reduce impacts of fish waste and excess feed on surrounding environments. If the cage is located too close to a coral reef, effluents or derelict gear from the farm can sink to the seafloor and negatively impact the benthic environment. Additionally, if the cage is located in a shallow area above a seagrass bed, the cage has the potential to shade the seagrass and impact it’s growth and photosynthesis. ref  See the Water Pollution section for more information on optimal depth.


  • Ensure that there are no sensitive habitats directly under the cages. If possible, select areas that are mostly sandy and not adjacent to sensitive areas.
  • Select a site that has appropriate depth and current for the cages
  • Site farms at a minimum of twice the depth from the bottom of the cage



Different types of gear and cage types can be used depending on the geography, specific site, selected species, size of operation, and funding available. If aquaculture gear is not designed properly, is of poor quality, or is not serviced regularly,  it may detach or break from the cage and negatively impact local habitats, marine mammals, or travelling vessels. ref Depending on the gear and location, predators may be able to bite through the net to prey upon and damage the cultured fish. However, if properly designed, sited, and maintained, cages can last for years without needing replacement.


  • Take efforts to prevent predators from damaging gear and consider utilizing marine mammal deterring devices, only as appropriate and recommended by scientists knowledgeable about local conditions and ecosystems
  • Use high quality gear and ropes that are designed to reduce minimize entanglement and predation from marine animals
  • Develop and follow a standardized protocol for routinely monitoring and maintaining the cages and gear
  • Follow proper boating protocols when accessing and maintaining the cages in order to minimize interactions with marine mammals and protected species



Regulations should govern proper siting of finfish cages in the marine environment, and include requirements for monitoring, although this may not be the case in some countries. It is imperative to carry out monitoring of farm effluent, nearby water quality, and farm impacts during the production cycle to observe and record any habitat impacts that may be occurring. ref A good resource on monitoring aquaculture effluent is opens in a new windowGuidelines on a Harmonized Environmental Monitoring Programme (EMP) for Marine Finfish Cage Farming in the Mediterranean and the Black Seaopens PDF file . An important aspect of monitoring is conducting a baseline assessment before installing any cage or gear to know what kind of changes occur during construction and operation of the cages.


  • Establish a baseline of conditions in the farm area before placing farms so that any future impacts can be quantitatively assessed
  • Establish better management practices for the farm and create a farm monitoring plan
  • Conduct regular monitoring of the farm to assess whether habitat impacts are occurring - methods could include video, photos, and seafloor sampling via diving.


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