Aquatic and marine dead zones can be caused by an increase in nutrients (particularly  nitrogen and phosphorus) in the water, known as eutrophication. These nutrients are the fundamental building blocks of single-celled, plant-like organisms that live in the water column, and whose growth is limited in part by the availability of these materials. With more available nutrients, single-celled aquatic organisms (such as algae and cyanobacteria) have the resources necessary to exceed their previous growth limit and begin to multiply at an exponential rate. Exponential growth leads to rapid increases in the density of certain types of these phytoplankton, a phenomenon known as an algal bloom.
Limnologist David Schindler, whose research at the Experimental Lakes Area led to the banning of harmful phosphates in detergents, warned about algal blooms and dead zones, 
The major groups of algae are cyanobacteria, green algae, dinoflagellates, coccolithophores and diatom algae. An increase in the input of nitrogen and phosphorus generally causes cyanobacteria to bloom. Other algae are consumed and thus do not accumulate to the same extent as cyanobacteria. Cyanobacteria are not good food for zooplankton and fish and hence accumulate in water, die, and then decompose. The bacterial degradation of their biomass consumes the oxygen in the water, thereby creating the state of hypoxia.
Dead zones can be caused by natural and by anthropogenic factors. Natural causes include coastal upwelling, changes in wind, and water circulation patterns. Other environmental factors that determine the occurrence or intensity of a dead zone include long water residence times, high temperatures, and high levels of sunlight penetration through the water column.
Additionally, natural oceanographic phenomena can cause deoxygenation of parts of the water column. For example, enclosed bodies of water, such as fjords or the Black Sea, have shallow sills at their entrances, causing water to be trapped there for a long time. The eastern tropical Pacific Ocean and northern Indian Ocean have lowered oxygen concentrations which are thought to be in regions where there is minimal circulation to replace the oxygen that is consumed. These areas are also known as oxygen minimum zones (OMZ). In many cases, OMZs are permanent or semi-permanent areas.
Remains of organisms found within sediment layers near the mouth of the Mississippi River indicate four hypoxic events before the advent of synthetic fertilizer. In these sediment layers, anoxia-tolerant species are the most prevalent remains found. The periods indicated by the sediment record correspond to historic records of high river flow recorded by instruments at Vicksburg, Mississippi.
Changes in ocean circulation triggered by ongoing climate change could also add or magnify other causes of oxygen reductions in the ocean.
Anthropogenic causes include use of chemical fertilizers and their subsequent presence in water runoff and groundwater, direct sewage discharge into rivers and lakes, and nutrient discharge into groundwater from large, accumulated quantities of animal waste. Use of chemical fertilizers is considered the major human-related cause of dead zones around the world. However, runoff from sewage, urban land use, and fertilizers can also contribute to eutrophication.
In August 2017, a report suggested that the US meat industry and agroeconomic system are predominantly responsible for the largest-ever dead zone in the Gulf of Mexico.  Soil runoff and leached nitrate, exacerbated by agricultural land management and tillage practices as well as manure and synthetic fertilizer usage, contaminated water from the Heartland to the Gulf of Mexico. A large portion of the plant matter by-products from crops grown in this region are used as major feed components in the production of meat animals for agribusiness companies, like Tyson and Smithfield Foods. Over 86% of the livestock feed is inedible for humans.
Notable dead zones in the United States include the northern Gulf of Mexico region, surrounding the outfall of the Mississippi River, the coastal regions of the Pacific Northwest, and the Elizabeth River in Virginia Beach, all of which have been shown to be recurring events over the last several years. Around the world, dead zones have developed in continental seas, such as the Baltic Sea, Kattegat, Black Sea, Gulf of Mexico, and East China Sea, all of which are major fishery areas.