One response to added amounts of nutrients in aquatic ecosystems is the rapid growth of microscopic algae, creating an algal bloom. In freshwater ecosystems, the formation of floating algal blooms are commonly nitrogen-fixing cyanobacteria (blue-green algae). This outcome is favored when soluble nitrogen becomes limiting and phosphorus inputs remain significant. Nutrient pollution is a major cause of algal blooms and excess growth of other aquatic plants leading to overcrowding competition for sunlight, space, and oxygen. Increased competition for the added nutrients can cause potential disruption to entire ecosystems and food webs, as well as a loss of habitat, and biodiversity of species.
When overproduced macrophytes and algae die in eutrophic water, their decompose further consumes dissolved oxygen. The depleted oxygen levels in turn may lead to fish kills and a range of other effects reducing biodiversity. Nutrients may become concentrated in an anoxic zone, often in deeper waters cut off by stratification of the water column and may only be made available again during autumn turn-over in temperate areas or in conditions of turbulent flow. The dead algae and organic load carried by the water inflows into a lake settle to the bottom and undergo anaerobic digestion releasing greenhouse gases such as methane and CO. Some of the methane gas may be oxidised by anaerobic methane oxidation bacteria such as Methylococcus capsulatus, which in turn may provide a food source for zooplankton.  Thus a self-sustaining biological process can take place to generate primary food source for the phytoplankton and zooplankton depending on the availability of adequate dissolved oxygen in the water body.
Enhanced growth of aquatic vegetation, phytoplankton and algal blooms disrupts normal functioning of the ecosystem, causing a variety of problems such as a lack of oxygen which is needed for fish and shellfish to survive. The growth of dense algae in surface waters can shade the deeper water and reduce the viability of benthic shelter plants with resultant impacts on the wider ecosystem. Eutrophication also decreases the value of rivers, lakes and aesthetic enjoyment. Health problems can occur where eutrophic conditions interfere with drinking water treatment.
Phosphorus is often regarded as the main culprit in cases of eutrophication in lakes subjected to "point source" pollution from sewage pipes.  The concentration of algae and the trophic state of lakes correspond well to phosphorus levels in water. Studies conducted in the Experimental Lakes Area in Ontario have shown a relationship between the addition of phosphorus and the rate of eutrophication. Later stages of eutrophication lead to blooms of nitrogen-fixing cyanobacteria limited solely by the phosphorus concentration.  Phosphorus-base eutrophication in fresh water lakes has been addressed in several cases.