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Water quality is a term used to describe the chemical, physical, and biological characteristics of water, usually in respect to its suitability for a particular purpose.

Bacteria and microorganisms have gotten into drinking-water supplies, sometimes causing severe illness in a town; chemical pollutants have been detected in streams, endangering plant and animal life; sewage spills have occurred, forcing people to boil their drinking water; pesticides and other chemicals have seeped into the ground and have harmed the water in aquifers; and, runoff containing pollutants from roads and parking lots have affected the water quality of urban streams.

Medium- to large-scale agricultural operations can generate in animal feed, purchased fertilizer, and manure, more nitrogen and phosphorus than can be used by crops or animals. These excess nutrients have the potential to degrade water quality if incorporated into runoff from farms into streams and lakes

It is primarily caused by the leaching of phosphate or nitrate containing fertilisers into lakes or rivers. Some algae and blue-green bacteria thrive on the excess ions and a population explosion known as algal bloom occurs. This growth is unsustainable, however. Perhaps because another nutrient becomes limiting, massive death among the bacteria happens, and they float to the surface.

Oxygen is required by all respiring animals in the water and it is replenished by photosynthesis of green plants. The oxygen level is already low because of the population explosion and further oxygen is taken up by microorganisms which feed off the dead algae. The layer of dead algae also forms a surface layer through which little light can pass, meaning the rate of photosynthesis decreases and the oxygen level becomes depleted. Due to this, fish suffocate.

Freshwater algal blooms are the result of an excess of nutrients, particularly phosphorus.[1] The excess of nutrients may originate from fertilizers that are applied to land for agricultural or recreational purposes, these nutrients can then enter watersheds through water runoff.

When phosphates are introduced into water systems, higher concentrations cause increased growth of algae and plants. Algae tend to grow very quickly under high nutrient availability, but each alga is short-lived, and the result is a high concentration of dead organic matter which starts to decay. The decay process consumes dissolved oxygen in the water, resulting in hypoxic conditions. Without sufficient dissolved oxygen in the water, animals and plants may die off in large numbers.

The EPA water quality criteria state that phosphates should not exceed .05 mg/l if streams discharge into lakes or reservoirs, .025 mg/l within a lake or reservoir, and .1 mg/l in streams or flowing waters not discharging into lakes or reservoirs to control algal growth (USEPA, 1986). Surface waters that are maintained at .01 to .03 mg/l of total phosphorus tend to remain uncontaminated by algal blooms.

Why are high nitrate or nitrogen concentrations in water a problem, and what can be done to maintain safe levels?

Excessive concentrations of nitrate in lakes and streams greater than about 5 milligrams per liter (measured as nitrogen), depending on the water body, can cause excessive growth of algae and other plants, leading to accelerated eutrophication or "aging" of lakes, and occasional loss of dissolved oxygen.

However, excess levels of nitrates in water can create conditions that make it difficult for aquatic insects or fish to survive.

Algae and other plants use nitrates as a source of food.  If algae have an unlimited source of nitrates, their growth is unchecked.

Coho salmon (Oncorhynchus kisutch) tend to spawn in small streams where the flow is 2.9–3.4 cfs.

Humans can impact the flow regime in three ways: controlling natural flow, increasing flow (adding water to the system), and decreasing flow (removing water from the system).

While potentially deleterious to the earliest life stages, flood events are essential to the development and maintenance of healthy stream systems. Floods change the stream structure by altering the active channel, creating new side channels, and recruiting and transporting large woody debris. Flood events bring new sediment to replenish stream banks, and fresh seeds and propagules to colonize open soils. High flows carry coarse sediment and deposit gravel in downstream reaches while flushing fine sediment from spawning gravel. While a severe flood year may result in a low survival rate for the present year cohort of salmonids, the resulting habitat changes can create improved habitat for future generations.

Streamflow is a key factor affecting the quality of salmon's freshwater habitat. Although the benefits to salmon for a specific increase in streamflows are difficult to assess precisely, biologists point to substantial scientific evidence that reductions in flows have contributed to the decline in salmon stocks throughout the region. Thus, a critical issue in the current policy setting will be how to maintain adequate streamflows to protect existing freshwater habitats and restore those that have been degraded.