Introduction to Water Quality

Color, taste, or odor can indicate serious water quality problems—such as inputs of wastewater from tanning operations, corrosion of lead-containing pipes, or the presence of harmful cyanobacterial toxins—but can also be relatively harmless. Regardless, most people are understandably loath to drink water with any noticeable color, taste, or odor.

As low points on the landscape, water bodies are often the resting place for trash of various kinds, including floatables: pieces of litter that float on the water surface, such as bottles or plastic bags. Trash poses both an aesthetic problem and an ecological one, as birds and aquatic animals can become physically entrapped or smothered. In addition, there is growing concern over microscopic plastic particles (microplastics: <5mm; nanoplastics: <1mm), often derived from breakdown of larger plastics. These particles are small enough that they remain suspended in the water column, can be consumed by aquatic organisms, and are not efficiently removed by drinking water treatment; indeed, microplastics have recently been found in drinking water supplies as well as natural water bodies. The health effects of microplastics on people and animals are poorly understood.

Anthropogenic temperature deviations—especially increases—can affect habitat suitability, especially for cold-water fish. The main sources of temperature increases include the discharge of cooling water from power plants, the flow of stormwater over hot impervious surfaces (e.g., parking lots), and the removal of streamside vegetation and the shading that it provides. Anthropogenic climate change also causes waters to warm, with a recent study suggesting that by 2100, 10% to 60% of fish species will find themselves outside their thermal tolerance for reproduction, depending on how bad warming gets (Dahlke et al. 2020).

Natural waters have a balance between acids and bases, resulting in a pH that is usually close to neutral (generally between 5 and 9, where 7 is neutral). Discharges of highly acidic (low pH) or basic/alkaline (high pH) effluents from industrial processes can kill fish and other organisms. Mining operations often lead to formation of highly acidic water (acid mine drainage) from the reaction of oxygen with iron and sulfide minerals that are newly exposed to air. Acid mine drainage can have very high concentrations of iron and other metals, since acidity generally increases metal solubility. Depending on the geology, mining can also produce alkaline mine drainage, usually from reaction with limestone and other base-producing rocks.

As the name implies, TDS is the sum of all the material dissolved in the water, expressed in milligrams of dissolved solids per L of water (mg/L). The bulk of the dissolved material consists of highly soluble ions, largely derived from rock weathering: the cations (positively charged ions) Na⁺, K⁺, Mg²⁺, Ca²⁺, and the anions (negatively charged ions) Cl^-, SO₄^2-, and HCO₃^-. When TDS rises above ~1,000 mg/L, we often switch to the term salinity, which—like TDS—refers to the total concentration of dissolved salts, but is usually expressed in g of salt per kg of water, also known as parts-per-thousand, given the symbol ‰. Both TDS and salinity can be monitored easily in the field using a conductivity meter, which measures the ability of the ions in the water to conduct a current. Water bodies vary naturally in their TDS/salinity from very dilute to very concentrated (see table below). However, human activity can increase the salinity of fresh waters in various ways. Unlike sediment or organic material, salts are hard to remove from water since they are highly soluble and non-degradable.

Approximate salinity ranges for water bodies. These terms, especially “brackish,” are not rigidly defined and are used differently in different contexts.

Hard water has relatively high levels of the divalent (doubly-charged) cations Ca²⁺ and Mg²⁺. While this is a natural characteristic of many water bodies and is not harmful to human or ecosystem health, hard water does pose problems for household use, as it can lead to formation of CaCO₃ scale on hot-water pipes and reduce the cleaning efficiency of soaps.

These five parameters are different measures of the sediment suspended in the water column. (See here for a primer on suspended, colloidal, and dissolved material in water.) Turbidity (cloudiness) is assessed by measuring the scattering of light by particles in the water, while TSS and SPM are mass measurements (mg/L) of the amount of material captured by filters. Secchi depth, mostly used in lakes, is the depth at which a Secchi disk can no longer be seen; the larger this number, the clearer the water is. Settleable solids are measured by letting the water sample sit undisturbed for an hour in a tapered container called an Imhoff cone, and then measuring the volume of solids that have settled to the bottom of the cone. 

Suspended sediment levels vary naturally from site to site and over time; most rivers (even pristine ones) experience much higher turbidity during storm events, when flows are high enough to erode both watershed soils and the streambed itself. Many human actions can increase sediment loads, including discharge of municipal or industrial effluents and erosion of poorly-protected agricultural or urban soils. In addition, dams can trap sediments and lead to unnaturally clear water downstream, which can impact both physical and ecological processes. 

An adequate level of oxygen dissolved in the water column is vital for most aquatic organisms. Oxygen concentrations in a water body are controlled by both physical and biological processes. Physically, aeration of the water (good contact between the water and the air) tends to lead to 100% oxygen saturation, that is, to an oxygen concentration that reflects the physical-chemical equilibrium between oxygen in the air and oxygen in the water. The amount of oxygen dissolved in water at 100% saturation is dependent on temperature and salinity, and ranges from ~6 mg/L at high temperature and high salinity to ~14 mg/L at low temperature and low salinity. 

However, the actual oxygen concentration in a water body can differ significantly from this saturation level. In particular, photosynthesis (which produces O₂; see this primer) can lead to super-saturation (high levels of DO), while respiration (which consumes O₂) can lead to under-saturation (low levels). Anthropogenic inputs of organic matter, such as sewage or other organic wastes, can increase respiration rates, resulting in hypoxia (low DO) or anoxia (no DO), with severe impacts to fish and other higher organisms. Hypoxia and anoxia are most likely in water masses that have slow rates of re-aeration, either because they are stagnant or because they are isolated from the atmosphere by stratification. In addition, water-saturated soils with high organic matter content, as in wetlands, tend to experience low O₂ conditions, because O₂ resupply is slow when pores are filled with water rather than air. Anoxic soils and water bodies are hot spots for anaerobic respiration.

These measures all reflect the amount of organic matter in a water sample, with the first two specifically related to the oxygen-depletion potential of that organic matter. High levels of organic matter may originate from either natural (e.g., decomposing leaves) or anthropogenic (e.g., sewage) sources, and can cause hypoxia downstream.

BOD is measured by incubating a water sample in the dark for 5 days and allowing bacteria to respire the organic matter and in the process consume oxygen; the difference in oxygen concentration between the beginning and end of the 5-day incubation is the BOD5, expressed in mg O₂/L. COD is similar, except that the oxygen consumption is carried out by chemical, rather than biological, oxidation. TOC is a direct measure of the organic matter present in the water sample (expressed as the amount of carbon, the main constituent of organic compounds). TOC is generally positively related to BOD and COD, but the relationship differs from sample to sample, since not all the TOC is available for oxidation. DOC is the fraction of TOC that is dissolved (i.e., goes through a filter). 

In order to grow, photosynthetic organisms need certain amounts of inorganic nutrients, especially nitrogen (N) and phosphorus (P). The presence of elevated levels of these nutrients in a water body—referred to as eutrophication—can lead to abnormally high rates of photosynthesis, which can have several negative effects, including algal blooms and ultimately hypoxia (caused by subsequent respiration of the increased organic matter production). 

In fresh water, P tends to be the limiting nutrient (the nutrient present in lowest supply relative to need and thus the nutrient whose addition will lead to algal blooms), while N is usually limiting in brackish and salt water. Human activities have greatly accelerated the natural cycles of N and P, and increased the availability of these nutrients in many water bodies. For more on nutrient cycling, see this primer. 

While high nutrient concentrations may indicate the potential for an algal bloom, the actual amounts of floating photosynthetic organisms (referred to as phytoplankton) are often assessed using the concentration of chlorophyll a, a photosynthetic pigment. Harmful algal blooms (HABs)—colloquially called “red tides” even though they aren’t always red and can occur in lakes as well as coastal waters—are large blooms that have toxic or otherwise noxious effects on people or other organisms. HABs are favored by high N and P levels and high water temperatures, and generally consist of a single species (in each bloom), often a species of dinoflagellate (a category of microalgae) or cyanobacterium (a group of photosynthetic bacteria that are not technically algae but are generally included in the term “algal bloom”). Cyanobacteria produce chemicals known as cyanotoxins, which are toxic to people, pets, and wildlife. 

Human and animal excreta can contain pathogens that can transmit infectious diseases. To identify the possible presence of pathogens in water, we use several indicator bacteria: bacterial groups that are not in themselves harmful, but that are relatively easy to measure and that tend to co-occur with fecal pathogens. When concentrations of these indicators go above established thresholds, we consider the water potentially contaminated with pathogens and unsafe to use. Different indicators are used for different applications, e.g., drinking water, swimming, etc. The most important indicator groups are:

Total coliform: a large group of bacteria, used to indicate possible water quality problems in drinking water and to require more specific testing.

Fecal coliform: a subset of total coliform that is a bit more specific to human/animal waste, used in some countries for testing of both drinking water and bathing beaches.

Escherichia coli (E. coli): a subset of fecal coliform that is well-correlated with the presence of pathogen-related illness and is used in the US as the primary indicator for freshwater bathing beaches.

Enterococci: a group of bacteria found in feces that is used in the US as the primary indicator for saltwater bathing beaches.

Radionuclides are atoms whose nuclei are unstable and are undergoing radioactive decay, in the process releasing radiation (gamma rays) and/or energetic particles (alpha and beta particles) that can damage human tissue. Three important sources of radionuclides to water are: erosion of soil or sediment that naturally contains radionuclides; routine or catastrophic releases from nuclear power plants; and hard-rock mining and oil and gas recovery, which can mobilize naturally occurring radionuclides in the subsurface.

Trace metals are metallic and semi-metallic elements that occur naturally at relatively low concentrations (i.e., excluding the major metals K, Na, Mg, Ca, and the semi-major metals Fe and Al). Some of these elements are essential micro-nutrients, some are toxic, and some are both, depending on dose. Trace metals are used in a variety of human activities and can end up in waterways at concentrations that are well above natural levels. Some of these metals tend to bioaccumulate in fish, so people can receive high doses from eating contaminated fish. Among the most important toxic trace metals are the following:

• Arsenic (As): At high doses, As is a well-known poison. Chronic exposure over many years to low-to-moderate doses of As can cause arsenicosis, characterized by severe skin lesions, skin cancer, and other fatal illnesses. Arsenic is used in industry and agriculture, but most human exposure is from drinking groundwater that is naturally high in As, found in several locations around the world, including Bangladesh, Vietnam, Argentina, and the western US.
• Mercury (Hg): Hg is an unusual metal in that it is a liquid at room temperature and can also be found in the gas phase. Hg is a neurotoxin whose toxicity depends on its speciation (how oxidized it is and what it is bound to), with methylmercury being the form of greatest concern, and seafood often representing the greatest exposure. Historically, Hg has had a wide variety of uses, including in batteries, thermometers, dental fillings, and the chlor-alkali process that is the basis of PVC plastics, but global use of Hg has declined due to its toxicity.
• Lead (Pb): Due to its malleability, Pb has long been a tempting choice for water pipes (even lending its Latin name, plumbum, to the word plumbing), but it is also a highly toxic metal that can cause developmental delays, high blood pressure, and many other effects, including premature death. Exposure to Pb in the US has dramatically decreased over the last several decades due to bans on leaded gasoline and lead paint, but exposure in drinking water is still a problem.

Organic pollutants are carbon-based compounds, but they differ from the bulk organic matter reflected in measures like BOD in that they are petroleum-derived or synthetic compounds, and are often toxic to people and/or other organisms. Organic pollutants also tend to be present at much lower concentrations than the natural or sewage-derived organic matter that makes up the bulk of BOD, so they are sometimes referred to as organic micropollutants. 

While some organic pollutants (e.g., benzene) break down fairly rapidly in the environment, others (e.g., polychlorinated biphenyls, known as PCBs) are persistent for long time periods. There are tens of thousands of synthetic organic compounds in use in industrialized societies, and we don’t have enough information on the environmental fate and toxicity of many of these. Many organic pollutants are hydrophobic, so they tend to accumulate in sediment (a process known as sorption) and in organisms (bioaccumulation), and the main pathway of human exposure is often from consumption of fish and other animal products. 

Five groupings of organic pollutants are worth highlighting:

• Oil: Oil spills are one situation where organic pollutants are not micro; catastrophic spills or blowouts can lead to large releases of petroleum, causing huge environmental damage. While most petroleum compounds are relatively degradable, some of the heavier compounds will stick around for a long time in the form of tarballs or sand patties. There are also lower-level chronic sources of petroleum, both from natural seeps and from human activities such as small spills at gas stations. Many urban waterways have significant concentrations of oil and grease—a measure of hydrophobic chemicals in water that includes cooking oils and animal fats as well as petroleum products.
• Disinfection byproducts: Disinfection of drinking water with Cl₂ or other chemicals leads to the formation of low concentrations of toxic disinfection byproducts: organic molecules formed by reaction of the disinfectant with naturally occurring organic matter.
• Pesticides: Most of the chemicals used to kill weeds (herbicides), insects (insecticides), or other pests are organic molecules. They range in environmental behavior from highly persistent to relatively degradable and from hydrophobic to water-soluble. Some—especially older chemicals like DDT—exhibit significant ecological and human toxicity.
• Persistent organic pollutants (POPs): These compounds—a set of pesticides and industrial chemicals—have an unfortunate combination of four characteristics that makes them a global health issue: persistence, toxicity, bioaccumulation, and the ability to be transported globally through air or water. The 2001 Stockholm Convention—an international treaty to ban or highly restrict POP use—originally focused on 12 POPs, but the list has since grown to include additional chemicals. All of the original “dirty dozen” were organochlorines: organic molecules containing chlorine, a feature common in industrial chemicals but rare in nature. The more recent additions include additional organochlorines but also three groups of brominated compounds (widely used as flame retardants and firefighting chemicals) and two fluorinated surfactants (surface-active agents that are useful as detergents, stain repellents, etc.): PFOA (perfluorooctanoic acid) and PFOS (perfluorooctanesulfonic acid). These fluorinated compounds are part of a larger group of “per- and poly-fluorinated substances” (PFAS), which are highly valued in industry for their unique properties, but which have been dubbed “forever chemicals” because of their persistence.
• Emerging contaminants: This term refers to chemicals that our monitoring and regulatory systems are just catching up to, i.e., chemicals that we are starting to find in the environment (and our bodies) but we are only starting to tackle as a problem. These emerging contaminants include the brominated and fluorinated compounds discussed above, as well as pharmaceuticals and personal care products, which often end up in waterways and can have biological effects at low concentrations. The emerging contaminants are only the most recent example of our evolving understanding of pollution. Again and again, we have become aware of a new type of potential chemical threat, started to look for it in our rivers and lakes and bodies, and indeed found it. This suggests that we need to start moving to a more precautionary approach, in which synthetic chemicals are designed to be non-toxic, or at least are evaluated for their harmful effects before we start using them.

Fluoride (F^-) provides a good illustration of Paracelsus’s maxim that “the dose makes the poison.” At low doses, fluoride appears to protect against dental cavities, and many water suppliers add fluoride to drinking water to provide this benefit. At higher doses, fluoride causes dental fluorosis, characterized by mottling and structural damage to the teeth; and skeletal fluorosis, characterized by increased bone density, with associated immobility, pain, and in extreme cases, deformities and paralysis. Some 200 million people around the world are at risk of fluorosis because they are drinking water with naturally-occurring high levels of F^- (Ayoob and Gupta 2006). While high fluoride is most commonly observed in groundwater, it can also be found in lakes, including the Rift Valley lakes in Kenya.