Eutrophication is where still or slow bodies, or parts of bodies, of water gain excess nutrients that weren't absorbed by the earth/living biomass. The nutrients stimulate excess plant growth (such as algae, or macrophytes, which are aquatic or semi-aquatic plants), resulting in a reduction of dissolved oxygen (hypoxic) in the water chemistry, suffocating the oxygen using aquatic animal life, especially immobile ones like fixed shellfish. The dead algae, bacteria, and fish sink to the bottom thus escalating the toxic fermenting nutritive situation. Also, some of the algae and bacteria (like cyanobacteria) are toxic, and get into the food chain, building up through to the predators (such as humans), damaging or killing them. It works like a negative feedback loop.
Where do these extra nutrients come from? The two biggest problems is phosphorus and nitrogen from fertilisers and sewerage. Fertilisers leach into the ground water and then into the drains, river systems and ocean from lawns, golf courses and other grounds, and agriculture. Nitrogen seems to affect fresh water systems and phosphorus affects salt water systems. Since the 1950's, due to human activity, phosphorus on the earth's surface has been raised by 4 times. Let's look at these chemicals.
Phosphorus is mined as apatite, a mineral compound. It is dissolved in sulfuric acid, releasing the phosphorus as a "super phosphorus", used in fertilisers. Animals eat plants and they absorb and excrete phosphorus, using it for ATP (energy utilisation), and it is a building block of RNA and DNA. Therefore phosphorus is found in excrement (sewerage and manure), which returns to the cycle, often through the waterways (these days).
Nitrogen is formed into ammonia in industry by putting atmospheric nitrogen and hydrogen (usually from natural gas or petroleum) under great pressure and 600 degrees Celsius. This is used in fertilisers.
It is also formed from lightning, created in the great heat and energy of the event. It is also formed by bacteria and archaea in symbiosis with legumes (etc. alfalfa, soy, lentils). It is also found in the digestive system of termites and bivalves like shipworms. It is also free in soils. Also cyanobacteria have it in places like rice paddies.
Nitrogen is very stable as N2, so biologically an organism needs complex enzymes and a lot of ATP (energy) to utilise it. Nitrifying bacteria make it available to plant roots and crenarchae converts ammonia into nitrites.
Anaerobic bacteria (anaerobic means it doesn't use oxygen) living in deep soil and aquatic sediment has the task of denitrification, because it uses the nitrogen instead of oxygen. However, it is a slow process.
There are 375 hypoxic (oxygen depleted) coastal zones around the world. The results is an increased biomass of phytoplankton including toxic and inedible ones and an increase of soft, sticky zooplankton (phytoplankton predators). There is a decrease of beneficial algae, and macrophyte (aquatic plants) species change in range and amounts. The water becomes turbid (unclear), often getting blue, green or red blooms (often blocking out the light, which effects other plants). It looks and smells bad, and is difficult to treat, and the water's oxygen is reduced (especially at night when the plants breathe out carbon dioxide). Good, edible and harvestable shellfish and fish start dying off. It becomes dangerous to drink and swim in. The toxic anaerobic bacteria increase, poisoning fish, animals and birds. Extremes create "dead zones". The biodiversity is reduced, and species that prefer the new conditions start to invade (such as jellyfish in the ocean between China and Japan, which only the tough and virile would eat). Toxic algae blooms form, poisoning the food chain, with predators becoming diahorrhoetic, neurotoxic, and paralysed.
There are several things that can be done to reverse this situation. Firstly identifying the source is a good start. A point source is something definite such as a feedlot (that's where they keep livestock in a confined area, feeding them large amounts of food to fatten them, a cruel system which creates a lot of waste), or a raw sewerage pipe. Non point sources are things like the atmosphere (such as acid rain), or runoff (like when thawing snow takes manure into the storm drain).
Legislation for local and regional areas can protect particularly vulnerable areas such as lakes, estuaries and bays. If the farmers, fishers, sewerage treatment, water and dam workers co-operate, they reduce the risks to their interdependent industries. However, more remote places can be harder to police.
Riparian buffer zones along the banks of waterways act as a biomass that absorbs the sediments, nutrients and pollutants. This idea can be extended to buffer zones around farms, storm drains and roads, or between them and waterways. If the farmer also grows their orchards closer to waterways, and their crops of smaller plants (like grains) further away, it can have a riparian effect, as well as having the effect that the thirstier (usually bigger) plants are closer to the water source, saving time, energy and effort.
Using sewerage to run methane burning generators, especially in rural communities and large farms is a great system, as it provides electricity, reduces carbon waste, deals with the nitrogen and phosphorus, and provides a wonderful recycled fertiliser. China has established these already.
Nitrogen testing and modelling of the soil helps too. Often farmers, gardeners and groundskeepers use more fertilisers then they need to, which is wasteful and costly. Testing the soil to work out the least amount needed is very economical.
The farmer can also charge more for their products if they actually convert to the very fashionable organic farming, where demand still outstrips supply, so the grower can dictate prices, as opposed having the prices set for them by competition or a corporation.
Maintaining and protecting marshes and mangroves in estuaries etc is a natural filter. If they are damaged, drained or otherwise removed, there is nothing there to prevent silt, nutrients and erosion from wrecking havoc. They are a wonderful kind of halfway world where little fish hatch and feed in bizarre safety, like a surrealistic dream!
Because of the phytoplankton and alga outbreaks, introducing herbivore animals like bivalve shellfish to filter the plankton and then harvesting them is a great way to reduce the nutrients.
Adding beneficial macrophytes (aquatic plants), and macroalgae (seaweed), and then harvesting them is also a way to remove the nutrients from the cycle. Large coastal kelp forests with kelp grazers would be most effective. Reeds (some reeds absorb heavy metals), watercress, lilies, rice and seaweed are all cash crops.
If you allow reeds to grow in the marshlands and rivers, introducing or encouraging birds that eat micro-organisms (like a mud filter type thing) and use reeds to build their nests would be optimum. Also, insects that eat or otherwise harvest reeds are a good idea.
In the case of cyanobacteria, which lives in deep silt at the bottom, and is toxic, surely it has a predator? Looking for something in deep water like volcanic lakes may provide answers, as well as researching "bottom feeders" like catfish (probably not a likely candidate) or specialist worms who sift through deposits for food.
Introducing of extra useful and edible zooplankton and maybe krill could also reduce phytoplankton and algae blooms. They may need extra oxygen though. Agrobacteria reduce nitrates and give plants galls on their stems. However, adding species is an activity that needs a lot of thinking through, research and planning before being undertaken, as it can have unhealthy results if it has the wrong effect, such as the South American cane toads of Australia.
Oxygenating the water is another option, through pumping air or pure oxygen through the water or something like a watermill to stir the air through and to break up the stagnation could reduce the anaerobic build up.
Damming decreases silica going downstream in the silt, and added fertilisers creates cyanobacteria blooms, increasing toxicity. A ratio range of N:P:Si (1:1:16) is the best for maintaining the nutritive balance for a healthy biodiversity. Allowing tides and natural "flushing" from both up and down stream to flow uninterrupted increases high species diversity, by increasing edible phytoplankton species for zooplankton to graze upon, and so reducing blooms. Erosion and damming prevent flushing from either end, causing build up and stagnation. If there is damming, it could be flushed regularly to increase healthy ecology, or else the water gets "old" and bad. Build up can be cleared, rivers widened and bottlenecks opened.
Erosion also contributes to the excess nutrients in the water, so riparian buffer zones are essential. Personally I think if we continue to use chemicals the riparian buffer zones could be twice as wide. Stabilising dunes with appropriate living biomass on the coastal areas helps reduce erosion. Sand fences work sometimes temporarily, and it is useful to pin netting down to help establish seedlings such as sand grasses.
Anyway, there are some ideas. There are probably other ideas, however, if you use a little lateral logic. Just letting the natural world be and do it's own thing unmeddled with (just undo the permanent meddling artifacts) would probably be the best option, as it has amazing self healing powers and many blocks and checks built over many millennia to restore balance. However, that seems to be against the force of human nature. We always seem to try to "improve" things to pieces!