Water Quality

Fish Aquaculture @TNC

Water quality around aquaculture farms is a very important factor for overall ecosystem health and the operational success of the farm. For fed species like finfish, excess feed can turn into dissolved nitrogen and phosphorus and cause impacts to benthic communities. Sensitive habitats such as coral reefs, seagrasses, and mangroves can be also damaged by excess nutrients in the water, which can stimulate algae blooms.

Larger numbers/densities of fish cages have a greater potential to result in water degradation. While some areas may be able to support a smaller number of cages without negative water impacts, increasing the number of cages or stocking higher densities of fish can create excess nutrients that the nearby environment cannot absorb sustainably. When in excess, these nutrients can potentially cause damaging effects, in the form of algal overgrowth and eutrophication, which now affects a large share of coastal waterbodies worldwide. As a general principle, it is important to limit the number of cages in small areas where the released nitrogen and phosphorus could be detrimental to the local ecosystem.

It is also important to note that except in localized examples, aquaculture is not generally the principal source of nutrients or cause of eutrophication in coastal waterways. Agriculture and runoff from populated areas are generally the largest contributors to eutrophication. However, in some circumstances, aquaculture has played a significant role and has shown to contribute as much as 10% of nitrogen loading and 26% of phosphorus loading in individual sites. ref

Water quality impacts from poorly sited finfish aquaculture. Image © Michael L. Webe, SeaWeb Aquaculture Clearing House


While aquaculture can be detrimental to water quality, it can also be part of the solution. Both algae and bivalve (such as oysters, mussels, and clams) mariculture can sequester excess nutrients from the water column, helping to prevent eutrophication. ref Additionally, bivalves contribute to water clarity by filtering organic and particulate matter from the water column. ref Herbivorous finfish can also play a role in grazing on microalgae and phytoplankton that can cause algal blooms. Therefore, co-culture of finfish with algae or shellfish may be able to help remediate some of the nutrient pollution emitted from finfish farms. Seaweed mariculture has also been shown to help mitigate the effects of ocean acidification at a local level by sequestering carbon from the water column, and could potentially help protect coral reefs in the vicinity of a farm. ref

Seafloor Depth

A generally accepted depth for marine finfish cages is at least twice the depth of the bottom of the cage to have minimal impacts on water quality, benthic environment, and sensitive habitats. This recommended depth is dependent on local habitats and other factors. With lower current flow, a greater depth will allow for more effluent to be transported downstream and dissipate into the environment. Depending on the benthic environment, different anchoring systems will need to be evaluated to allow for the appropriate cage installation. ref Proper planning during site and cage type selection are essential in determining areas with appropriate seafloor depth.


  • Site farms at least twice the depth of the bottom of the cage (20-60 m)
  • Site farms in areas with greater currents (.05 - .2 m/s) and circulation


Proximity to Sensitive Habitats

A generally acceptable distance from corals is 200 meters to have minimal impacts on water quality, benthic environment, and sensitive habitats. This recommended distance is dependent on local habitats and other factors and is considered a conservative estimate. If aquaculture farms are directly on top of coral reefs or seagrasses and in shallow areas, farm infrastructure might obstruct sunlight reaching the coral or seagrass impacting photosynthesis. Even if reefs and seagrass are downstream of the farm, it is imperative to evaluate the speed of currents to determine if effluent will reach and negatively impact these environments. Mangroves are also important habitats for reef animals as they provide shelter and nursery grounds. Farms should not be placed in mangrove areas as nutrient accumulation might negatively affect the ecosystem. Similarly, proactive planning and regular monitoring needs to take place to evaluate whether there is current flow from cages into mangrove areas and, if so, the mangroves are able to absorb the additional nutrients. ref


  • Site farms at least 200 meters from coral reefs, mangroves, and sensitive habitats. Check and defer to local regulations as they may be more protective.
  • Engage in non-marine off-site stock processing in order to avoid excess waste falling into the water
  • Consider the use of integrated multi-trophic aquaculture, such as the co-culture of seaweed aquaculture in order to reduce excess nutrients within the surrounding water


Carrying Capacity

The concept that different aquatic environments can sustainably support a certain threshold of total fish weight is known as carrying capacity. If that carrying capacity threshold is passed, negative effects can occur that can jeopardize water quality and nearby habitats. There are many different methods and complex models that can explain and predict an environment's carrying capacity and thus the total farmed population that the environment can support. It is important to understand that carrying capacities differ between locations, depending on many factors, such as currents, natural flushing, depth, etc.

While conducting a carrying capacity study/creating a location-specific model is one of the most accurate ways to assess carrying capacity, these models are often expensive and require complex data sets that might not be readily available. As such, there are some countries that have employed alternate ways of setting limits on how much aquaculture can occur in the waterbody, such as setting a maximum percentage of water body that can be used for fed aquaculture or placing conditions on minimum distance between farms. Depth, currents, tides, feed type, feed quantity and selected species are factors that will affect the carrying capacity of an area. ref


  • If possible, conduct a carrying capacity study or model to help determine the overall impacts to water quality and upper limits for the stock density in a marine area
  • If a carrying capacity study or model is not possible, consider setting alternate conditions (e.g., a minimum distance between farms) to ensure that the amount of aquaculture infrastructure will not exceed the water body’s natural limits
  • Monitor for nutrients, water quality, and algae blooms


Water Currents and Circulation

Tidal flows and currents are an important aspect in siting proposed cages. Inward tides can transport cage nutrients closer to the coast and into mangroves, estuaries, and areas with denser populations, while outgoing tides can transport effluent towards the open ocean. Currents remove nutrients from the cage area and allow for oxygen-rich seawater to pass through the cage and provide the needed oxygen for the growing stock. Alternatively, aquaculture farms with no currents or sufficient tides will be stagnant and will not provide proper flushing. It is important to observe tide and current history to be able to predict how well proposed areas will be able to sustain aquaculture production. ref


  • Site farms in areas with greater currents (.05 - .2m/s) and circulation
  • Avoid the use of chemicals and antibiotics, if possible
  • Use non-chemical cleaning methods to clean and maintain infrastructure
  • If using chemicals, develop an action plan for responding to any chemical spills, including which government authorities to notify



Environmental monitoring should occur to determine whether the farm is impacting water quality. This monitoring should ideally include total suspended solids, water temperature, dissolved oxygen, salinity, nitrogen (ammonia, nitrate, nitrite), phosphorus, silicates, chlorophyll, and pH. At a minimum, monitoring should include measuring dissolved oxygen and ammonia. ref It is important to monitor these water quality parameters in various locations around the farm to determine how much the farm is impacting the local waters.


  • Establish a baseline study of and set limits for nutrients and water quality. While a suite of factors should ideally be assessed, establishing a baseline and setting limits for dissolved oxygen and ammonia are essential for marine finfish farming
  • Write and follow a monitoring plan to protect sensitive marine habitats such as corals, seagrasses, and mangroves
  • Ensure that any farm vessels used to operate or monitor farm are being maintained to prevent gasoline or oil leaks or spills


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