Terminology
Many of the terms in this glossary have broad definitions. The definitions used in this glossary, however, pertain primarily to the context in which they are used in this website.
List of water quality–impaired segments of water bodies subject to the Clean Water Act. Under Section 303(d) of the 1972 Clean Water Act, states, territories and authorized tribes are required to develop this list. Waters on the list do not meet water quality standards, even after minimum required levels of pollution control technology have been installed at point sources of pollution. The law requires that jurisdictions establish priority rankings for water bodies on the lists and develop action plans, called total maximum daily loads (TMDLs), to improve water quality and restore the water body to serve beneficial uses.
To adjust to changes in environmental conditions.
Temperature to which a fish has physiologically adjusted. When fish are exposed to a change in temperature, they require time to acclimate to that change. This usually involves a level of physiological adjustment to the new conditions, which is often accompanied by changes in physiological tolerance to other environmental factors. In laboratory testing of physiological parameters, fish are usually held in water with a constant temperature (the acclimation temperature) and allowed to acclimate prior to testing to avoid temperature-related changes in physiology which would complicate the results.
Amount of algae in a fixed volume of water (measured in mg/L). Live algal load is typically estimated using measurements of chlorophyll a, and detrital algal load is typically estimated using measurements of pheophytin pigment.
Habitats used by organisms when preferred habitats are uninhabitable or unavailable.
Biochemical process that converts organic nitrogen (i.e., nitrogen contained in organic chemicals in living or dead organic materials) to ammonia (NH3) or ammonium (NH4+). This process is carried out by ammonifying bacteria.
Bacteria that convert organic nitrogen (i.e., nitrogen contained in organic chemicals in living or dead organic materials) to ammonia.
Plan adopted by the regional water quality control board that sets standards for a variety of constituents of water quality, including DO concentrations (see regulatory minimum). The Water Quality Control Plan for the Sacramento River and San Joaquin River Basins contains standards for DO concentrations in the San Joaquin River. The long-term violation of these standards in the Stockton DWSC has led to its inclusion on the 303(d) list of impaired water bodies for DO.
Related to the bottom of a water body. A benthic fish is one whose primary habitat is the bottom of a water body. Generally, these fish are either lie-in-wait predators or species that move slowly over the bottom searching for food.
Biochemical oxygen demand (BOD)
Consumption (or decrease) of DO, caused either by microorganisms as they decompose organic material or by chemical oxidation. For the purpose of this conceptual model, BOD consists of two components: carbonaceous BOD and nitrogenous BOD. BOD levels are measured using laboratory tests.
Measure of BOD using a laboratory test that lasts a certain number of days: results based on tests lasting 5 days are denoted as BOD5 and results based on tests lasting 10 days are denoted as BOD10. Ultimate BOD is the BOD that would be consumed given an infinite amount of time (i.e., the total amount of oxygen consumed if the biochemical reaction was allowed to proceed to completion). The ultimate BOD is too time consuming, so BOD5 has almost universally been adopted as a measure of relative pollution effect.
Relatively high swimming speeds (greater than 10 body lengths per second) that can be maintained by fish for only very short periods (less than 20 seconds) (Beamish 1978). Burst speed is employed for feeding or escape, and represents maximum swimming speed (Biology-Online.org 2005). See also sustained swimming speed and cruise swimming speed.
Carbonaceous biochemical oxygen demand (CBOD)
Quantitative measure of the amount of oxygen required for the biological oxidation of carbonaceous (organic) material by microorganisms. The source material for CBOD is organic matter. In aquatic environments, organic matter is degraded by bacteria using biochemical processes that remove DO from the surrounding water.
Dimensions (i.e., depth, width, length) and shape of a river channel. Cross sections can be used to determine spatial variations in the width or depth of a river channel.
Measurement of living algae. Chlorophyll a is the only pigment in plants (aquatic plants and algae) capable of passing electrons and thereby producing the chemical energy in photosynthesis. The pigment is composed of four carbon-nitrogen rings surrounding a magnesium atom. See also pheophytin.
An organism that belongs in the same genus as another.
An herbivorous microscopic crustacean (subclass Copepoda), which is a food source for many fish species.
The temperature at which movement becomes disorganized and organisms lose their ability to escape from conditions promptly, leading to death.
Measurement of a river channel’s area (depth by width), measured perpendicular to the flow, at a specific location.
The speed that a fish can maintain for an extended period of time without fatigue (Biology-Online.org 2005). See also burst swimming speed and sustained swimming speed.
Removal of oxygen from water.
Deep Water Ship Channel (DWSC)
Portion of the San Joaquin River that has been altered by dredging to maintain a fixed depth of 35 feet and a minimum width of 250 feet to accommodate ship traffic for the Port of Stockton. The DWSC begins at Channel Point in Stockton and extends into San Francisco Bay.
Delta Simulation Model Version 2 (DSM2)
Mathematical model used for simulating tidal hydraulic and salinity conditions in the Sacramento–San Joaquin River Delta.
Decaying or decayed organic matter, including the remains of plants, animals, and their particulate waste products.
Biological transition of a fish from a simple to more complex form; usually marked by stages, such as egg, larvae, juvenile, and adult, that may accompany distinct physiological events, such as sexual maturation or smoltification. See also growth.
Compounds dissolved in water that are derived from organic material (i.e., plants and animals).
Oxygen molecules (O2) dissolved in water. Water has a capacity to hold DO, and this capacity increases with pressure (deeper water can hold more oxygen) and decreases with temperature (warmer water holds less oxygen). The availability of DO is important for fish, which take DO in through their gills, and for other aquatic species that require oxygen to live.
Reduction in the concentration of DO in a water body that occurs when those factors reducing oxygen concentrations outweigh those factors increasing oxygen concentrations.
Maximum concentration of DO that can be held in water, which depends primarily on water temperature and pressure. As water temperature increases, the DO saturation concentrations decreases because warm water cannot store as much DO as cold water. DO saturation increases directly with pressure. See also dissolved oxygen.
Difference between DO saturation and actual DO concentration caused by the consumption of DO by oxygen-demanding substances. The DO deficit is often the result of the presence of BOD. It can generally be described with the following simple equation:
DO deficit =
(BOD concentration [mg/L])
• (BOD decay rate [1/day])
• (decay time [days])
The basic measurement of BOD is the DO decline that is measured when water is held for 5 days in a dark bottle at 20°C. Because the BOD concentration decreases with time, a negative exponential equation is used to estimate the decay rate. See also Biochemical Oxygen Demand in the Basic Concepts page.
Marked decrease in DO concentrations below normoxia; these sags are usually low enough to cause negative biological impacts on fish and may be defined by a statutory minimum.
In the driver-linkage-outcome form of a conceptual model, a factor known to influence an outcome through a linkage mechanism. For example, photosynthesis is a driver for DO because the rate of photosynthesis of organisms in a water body directly affects the DO concentration. See also primary driver and secondary driver.
Water temperature at equilibrium with the temperature of the surrounding air.
Upper layer of a water body that receives enough sunlight to support photosynthesis. The euphotic zone varies by species.
Number of eggs in the ovaries of a female fish. Within a species or population, fecundity increases with the size of a fish.
The number of viable young produced.
Movement of water defined as the volume of water passing a point on the river in a given period of time. Often measured in cubic feet per second (cfs). Flow rates in the San Joaquin River are determined by the operation of upstream dams, natural hydrology, diversions from the river and its tributaries, return flows from agricultural and urban uses, and interactions between the river and adjacent groundwater basins.
Increase in size of an organism over time.
Deficiency of oxygen in the tissues of an organism, which may be caused by insufficient oxygen in the environment (hypoxic conditions).
Inability of a water body to support a beneficial use (e.g., drinking water, irrigation water, recreation, habitat) as a result of either excess levels of a harmful water quality constituent (e.g., heavy metals, pesticides) or insufficient levels of a beneficial one (e.g. DO).
In the driver-linkage-outcome form of a conceptual model, importance is an attribute of a linkage that indicates how much influence a driver has on the outcome. Importance is usually denoted in relative terms.
Oxygen concentration that causes 50% mortality during a specified period of time (typically 24- and 96-hour exposures). This threshold is the minimum oxygen concentration needed to sustain basal metabolic processes and varies among species.
Point below which DO concentrations limit the rate of oxygen uptake in an organism.
Line connecting points of equal value, such as DO concentrations or salinity, on a map or chart.
Fish that have the capability to spawn multiple times throughout their lives (e.g., sturgeon). See also semelparous.
Young fish, mostly similar in form to adult fish but not yet sexually mature (Hubbs 1943). In some cases, refers to a stage unlike the adult in appearance (Froese and Pauly 2006). In salmon, juvenile periods include stages such as parr and smolt.
Young fish that at birth or hatching is fundamentally unlike its parent and must pass through metamorphosis before assuming adult characteristics; a term covering developmental stages in the early life history of a fish between the time of hatching and transforming to a juvenile, the latter a miniature replica of the adult.
See lethal concentration.
Concentration of a water quality constituent, such as DO, that results in 50% mortality over a specified time period.
Chemical or physical environmental factors (e.g., nutrients, light, temperature, water) that control how much a species can grow or reproduce. Generally, the limiting factor can be determined by examining the abundance of all environmental conditions in relation to the minimum quantities or levels required for an organism’s uninhibited growth.
In the driver-linkage-outcome form of a conceptual model, the known or hypothesized mechanism by which the driver influences the outcome. For example, in the physical/chemical conceptual model for DO in the DWSC, CBOD is a primary driver. The linkage that connects CBOD concentrations with DO concentrations is the biochemical pathways that break down CBOD and consume oxygen, decreasing DO levels. Linkages also have attributes associated with them, including direction (i.e., increase or decrease), importance, and certainty. See also primary driver, secondary driver, importance, and uncertainty.
Mass (i.e., pounds [lbs] or kilograms) of a substance entering a water body in a given period of time (i.e., day). The San Joaquin River daily load of a substance can be calculated as:
load (lbs/day) =
5.4 • (concentration [mg/L])
• (flow [cfs])
where 5.4 is the combined conversion constant between these units. This simple relationship can be used to calculate the BOD load, the algae biomass load, or the DO load.
Stream of a fish’s birth.
Flow of the river if the tidal cycles were removed. In an estuary, river flows are complicated by the juxtaposition of tidal flow cycles on top of the river flows. For instance, water in the tidally influenced section of the San Joaquin River has a net flow toward the ocean, but water actually moves back and forth with the tides.
Chemical or biochemical process that converts nitrogen in the form of ammonia (NH3) to oxidized forms such as nitrites (NO2) and nitrates (NO3-). In water, this process uses (i.e., depletes) DO.
Bacteria in aquatic systems that convert ammonia to nitrites or nitrates, depleting DO in the process.
Nitrogenous biological oxygen demand (NBOD)
Quantitative measure of the amount of oxygen required for the biological oxidation of nitrogenous material, such as ammonia nitrogen and organic nitrogen. NBOD is usually calculated by subtracting CBOD from total BOD.
Sources of biomass other than algae, such as aquatic plants and dead plant and animal matter.
Normal levels of oxygen in the tissues of an organism (oxygen concentrations that allow full normal physiological function).
An element or compound required for metabolism. The primary nutrients required for algal growth are forms of nitrogen and phosphorus. The forms of nitrogen available for algae are nitrate, ammonia, and a portion of organic nitrogen that converts to ammonia. The form of phosphorus available for algae uptake is soluble orthophosphate.
In the driver-linkage-outcome form of a conceptual model, the environmental or physical conditions that are the target of management actions. For example, in the conceptual model for DO in the DWSC, DO concentration is the outcome. See also driver and linkage.
One half of a chemical reaction in which electrons are transferred from one substance to another. The oxidation half of the equation involves the loss of an electron. All oxidation reactions are paired with reduction reactions in which the lost electron is gained by another substance. Oxygen (O2) is a strongly oxidizing substance.
Fish and animals that live in open water away from shore and the bottom. Usually refers to oceanic species but can also apply to inland fish living in open water (such as delta smelt).
Degradation product resulting from the loss of a magnesium atom from a chlorophyll a pigment, which is used to measure the decay of algae.
Biochemical process carried out by plants in which light is converted to chemical energy stored as sugars. In the process, carbon dioxide (CO2), water, and light are used, and sugars and oxygen (O2) are generated.
In the driver-linkage-outcome form of a conceptual model, a factor known to influence the principle outcome through a linkage mechanism. For example, in the physical/chemical conceptual model for DO in the DWSC, DO concentrations are the primary outcome, and photosynthesis is a primary driver because the rate of photosynthesis by organisms in the water body directly affects the amount of DO. See also driver and secondary driver.
Segment of river or channel. The reaches used in these conceptual models are defined on the About this Conceptual Model page.
Transfer of oxygen from the air to a water body. Oxygen in the atmosphere exchanges with DO in the surface layer of water bodies. When water bodies have low levels of DO, the exchange tends to favor the movement toward the water and is called reaeration. The amount of reaeration depends on the amount of water surface area in contact with the atmosphere.
One half of a chemical reaction in which electrons are transferred from one substance to another. The reduction half involves the substance gaining an electron. All reduction reactions are paired with oxidation reactions in which a substance loses an electron.
In 1994, the State of California placed the San Joaquin River on the Clean Water Act Section 303(d) list of impaired water bodies because of low DO concentrations (Central Valley Regional Water Quality Control Board 1998), as well as other constituents not part of this conceptual model. DO concentrations continued to decline; in 1998, the state classified the issue as high priority for correction, placing a total maximum daily load (TMDL) requirement on the Stockton DWSC.
In response, a TMDL Implementation Program was developed, specifying that DO concentrations in the San Joaquin River between Turner Cut and Stockton should not fall below 5 mg/L from December through August and 6 mg/L from September 1 through the end of November.
Amount of time that a particle of water remains in a water body. Residence time is a measure of the amount of net flow in a river or lake because more flow will reduce the residence time in the river or lake. In the DWSC, residence time is controlled by the channel’s geometry (deep and wide) and the San Joaquin River inflows.
Residence time [days] =
volume [acre-feet]
/ daily flow [acre-feet].
Condition in which DO concentrations limit the rate of oxygen uptake from the surrounding water.
In the driver-linkage-outcome form of a conceptual model, a factor known to influence the outcome through an indirect linkage mechanism involving a primary driver. For example, in the physical/chemical conceptual model for DO in the DWSC, sunlight is a secondary driver because it influences DO concentrations indirectly by influencing the rate of photosynthesis, which, in turn, influences DO concentrations. See also driver, primary driver, and outcome.
Rate of oxygen consumption exerted on the overlying water by the sediments on the channel bottom. SOD is generated both by the oxidation of inorganic compounds, such as iron and sulfur contained in sediments, and by the decay of organic materials in the sediments.
Fish that are able to spawn only once during their lives (e.g., most salmon species). See also iteroparous.
Metabolic rate required for bare maintenance of bodily functions to sustain life.
Amount of water passed through the gills during each breathing stroke.
Resistance of a fish to the effects of pathogens or other harmful conditions.
Swimming speeds that can be maintained for long periods (more than 200 minutes) without muscle fatigue. See also burst swimming speed and cruising swimming speeds.
Total maximum daily load (TMDL)
Maximum amount of pollution that a water body can assimilate without violating state water quality standards. The process involved in developing a TMDL is described on the U.S. EPA’s website.
Amount of organic material in water, as measured by the carbon weight. This laboratory measurement is made by chemically converting all organic carbon molecules to CO2 gas, and measuring the mass of carbon released. The origin of total organic carbon is vegetation in the watershed and aquatic plants in rivers and streams. However, most organic carbon rapidly decays and releases CO2 to the atmosphere; only a small fraction (3–5%) of vegetation remains in the water as slowly decaying organic molecules, such as lignin, which are measured as total organic carbon.
Measure of the organic and nonorganic particulates in wastewater, effluent, or water bodies, determined by using tests for total suspended nonfilterable solids.
Amount of time required for a specified molecule of water to move from one point to another. Travel time depends on the distance between the two points, channel geometry, and river flow.
Transfer of food energy through levels of a food web.
A condition in water caused by the presence of suspended matter, resulting in the scattering and absorption of light. Turbidity limits the penetration of light into the water column, limiting the growth of organisms dependent on photosynthesis.
In the driver-linkage-outcome form of a conceptual model, an attribute of a linkage that indicates how well the relationship between the driver and the outcome is understood. Two types of uncertainty can be considered: uncertainty associated with a lack of scientific understanding of the mechanism and uncertainty associated with changes in the importance of a mechanism over time. Uncertainty is usually denoted in relative terms.
Amount of air inhaled in a specific time period. Also known as breathing rate or inhalation rate; in fish, this may refer to the frequency of breathing strokes passing water over the gills.
Vernalis Adaptive Management Program
Large-scale, long-term (12-year) experimental/management program initiated in 2000 and designed to protect juvenile Chinook salmon migrating from the San Joaquin River through the Sacramento–San Joaquin Delta. VAMP involves increasing flows in the San Joaquin River during the spring migration period of Chinook salmon (i.e., April 15–May 15). More information on VAMP is provided by the U.S. Fish and Wildlife Service.
volatile suspended solids (VSS)
Measurement of the organic particulates suspended in a water body or wastewater flow. VSS can be used to estimate BOD because it is composed of organic particulates that can decay and create an oxygen demand.
Range of an environmental variable (such as water temperature) that results in death of an organism in a certain period of time (e.g., 24 hours).
Range of an environmental variable (such as water temperature) that does not have direct lethal effects on an organism.