Algae are multi-cellular or single-celled aquatic plants and plant-like organisms. This large group includes phytoplankton, seaweeds, and lichens and can occur in both freshwater and saltwater. Algae primarily reside in light accessible regions of the water and generate oxygen via photosynthesis.

Ammonia (NH³) is an essential nutrient for many biological processes and  is present in plants and animals. As part of the nitrogen cycle, nitrifying bacteria convert ammonia into nitrate. Environmental sources of ammonia include human waste, animal waste, and agricultural fertilizers.  In aquatic environments, ammonia is a nutrient for algae and phytoplankton. 

Anoxia is the absence of oxygen. Aerobic organisms such as fish and shellfish are unable to survive in anoxic waters. Causes of anoxia include poor vertical water column mixing and rapid decomposition following phytoplankton blooms.

The benthos includes all animals and plants that live at the bottom of a body of water.

In aquatic environments, a bloom is the rapid growth of phytoplankton, resulting in high phytoplankton abundances and chlorophyll concentrations. Blooms occur when phytoplankton growth rates are lower than predator grazing rates, and can be caused by high nutrient concentrations fertilizing the phytoplankton. Blooms can be composed of one single species of phytoplankton or many species of phytoplankton. The resulting increase in organic matter can be very beneficial to the food web but may also contribute to hypoxic conditions upon decomposition.

Chlorophyll a is the green pigment used in the process of photosynthesis in plants (including algae) and some bacteria. Chlorophyll is measured in water bodies as a proxy for phytoplankton abundance. Lower chlorophyll concentrations indicate smaller phytoplankton populations while high chlorophyll concentrations indicate larger phytoplankton populations. 

The density of water is defined as its mass per unit volume. The density of water is affected by changes in temperature and salinity – cold water is more dense than warm, and salt water is more dense than fresh. Water masses with lower densities will layer above higher density water masses, which can cause vertical stratification. For example, in the summer we often observe a warm freshwater rain or river runoff layer sitting atop the cold, dense saltwater layer.

Dissolved oxygen (DO) is the amount of oxygen gas present in the water column. Sources of DO include photosynthesis and mixing at the water-air interface by wind and wave action. Oxygen is required by almost all organisms on earth, even those living in the water. 

Enterococci are a group of bacteria commonly found in the digestive tracts of humans and other animals. Enterococci concentrations are used as indicators of the potential health risk for individuals exposed to untreated wastewater, which may contain harmful pathogens. 

An estuary is a transition environment where freshwater meets the ocean. Examples of estuaries include bays, harbors, fjords, and river deltas. Estuaries are brackish with salinities ranging from 0-35 ppt. Estuaries tend to support high biological diversity and are very productive environments. Narragansett Bay is the largest estuary in New England.

Fecal coliform are a type of bacteria that are commonly found in the digestive tracts of humans and other animals. Fecal coliform concentrations are used as indicators of the potential health risk for individuals exposed to untreated wastewater, which may contain harmful pathogens. 

Harmful algal blooms (HABs) are bloom events of certain phytoplankton species which may have adverse effects on humans or other aquatic organisms when in large concentrations. Some HAB-forming species produce toxic chemicals while other HAB-forming species can cause mechanical damage to organisms. HAB events are associated with human health risks and aquatic mortality events.

Hypoxia is a term used to describe low dissolved oxygen conditions in the water column. Hypoxic conditions are commonly defined as dissolved oxygen concentrations of 2.9 mg/L or less. Causes of oxygen depletion include poor vertical water column mixing and rapid decomposition following phytoplankton blooms.

Nitrate

Nitrate (NO₃^-) is a naturally occurring nitrogen compound involved in the nitrogen cycle. Nitrate is formed through the decomposition of animal or human waste. More specifically, nitrifying bacteria oxidize nitrite to form nitrate. Nitrate is commonly used as a fertilizer, so agricultural runoff may cause high nitrate concentrations in rivers, estuaries, lakes, and oceans.

Nitrite (NO₂^-) is a naturally occurring nitrogen compound involved in the nitrogen cycle. Nitrite is formed through the decomposition of animal or human waste. In the nitrogen cycle, nitrifying bacteria oxidize ammonia to form nitrite. 

Non-point source pollution cannot be attributed to one specific output point. Non-point sources of pollution in the Narragansett Bay estuary include stormwater, urban runoff, fertilizers, and agricultural runoff.

Orthophosphate (PO₄) is a naturally occurring form of phosphorus. Phosphorus is a building block of life and plants need it to grow. Phosphorus is most biologically available to organisms in the form of orthophosphate. If excess phosphorus is present in water bodies, algal blooms may occur, potentially leading to conditions of low dissolved oxygen.

pH is a measure of the acidity or alkalinity (basicity) of a liquid solution, based on the concentration of hydrogen ions (H⁺) in the solution. This is measured using the pH scale which ranges from 0 to 14. The pH of a solution of pure water is 7, which is considered neutral. pH values from 7 to 14 are basic, or alkaline, while pH values from 0 to 7 are acidic. Most aquatic environments (streams, lakes, rivers, estuaries) range from 6 to 8 in pH and more acidic or basic waters may cause stress to aquatic organisms. 

The photic zone is the depth in the water column where a sufficient amount of light from the sun is able to penetrate and support photosynthesis. Below this depth, light conditions are too low to support photosynthesis.

Photosynthesis is the process in which plants, phytoplankton, and algae use the energy from the sun to convert carbon dioxide (CO₂) and water into oxygen (O₂) and sugar, which the plants, phytoplankton and algae use as food. The chemical equation used to express this process is: 

6 CO₂ + 6 H₂O -> C₆H₁₂O₆ + 6 O₂ 

Photosynthetically active radiation (PAR) is the amount of light available for photosynthesis, which is light in the 400 to 700 nanometer wavelength range. PAR changes seasonally and varies depending on the latitude and time of day. Light wavelengths within this range are used by phytoplankton to photosynthesize. Scientists measure PAR at different depths to see how much light penetrates the water column, which allows them to assess how much light is accessible to photosynthesizing organisms. Without adequate PAR, phytoplankton are unable to grow.

Phytoplankton are microscopic, single celled plants that drift with the currents in aquatic environments. Through photosynthesis, phytoplankton use solar energy, carbon dioxide, and water to produce carbohydrates for energy and oxygen. Just like plants on land, phytoplankton form the base of the food web in the ocean.

Plankton are organisms living in rivers, lakes, and oceans that drift with the currents. While some plankton can swim, they are unable to swim strongly enough to move independently of tides and currents. Plankton range in size from microscopic cells to jellyfish that can easily be observed with the naked eye. Plankton can be bacteria, plants, or animals.

Point source pollution originates at one specific output location. Examples of point source pollution include sewage discharge pipes and industrial discharges.

Salinity is the concentration of salt in water. Freshwater (rivers, streams, lakes) usually has a salinity of less than 0.5 ppt, whereas ocean water has an average salinity of 35 ppt. In estuaries, where freshwater meets ocean water, salinity can range anywhere between these concentrations. Tides, precipitation, and river flow can affect the salinity of an estuary like Narragansett Bay. Some organisms are adapted to live only within a certain salinity range while other organisms are adapted to a wider range of salinities. 

A Secchi disk is a simple tool used by scientists to measure water clarity. It consists of a small black and white disk which is lowered into the water. The depth at which the disk is no longer visible is recorded as the Secchi depth. Secchi depth is affected by the amount of particulate matter in the water, the time of day, the amount of sunlight, and cloud cover. Higher Secchi depths indicate better water clarity while lower Secchi depths indicate lower water clarity.

Silicate (H₄SiO₄) exists as a dissolved compound in water and is an essential nutrient for a group of phytoplankton called diatoms. Diatoms are characterized by a hard cell wall covering made of silica, called a frustule. Without silicate in the water, diatoms are unable to grow.

Stormwater is surface water resulting from rain and snowfall. In developed areas, stormwater runoff transports contaminants from paved surfaces including roads and sidewalks to local waterbodies. Stormwater runoff is a non-point pollution source that negatively impacts water quality.

Stratification of the water column occurs when water bodies with different physical properties form distinct layers that prevent water mixing. Stratification is usually caused by differences in temperature, salinity, or density. Prolonged periods of stratification can prevent the replenishment of dissolved oxygen in bottom waters, which can be detrimental to organisms.

Temperature is the physical measure of thermal energy, and is measured with a thermometer. Water temperature is an important parameter biologically and chemically. Some organisms are very sensitive to temperature and can survive only in a narrow temperature range. Additionally, the temperature of the water affects potential concentrations of dissolved oxygen water can hold. Finally, differences in temperature in the water column can lead to stratification.

Total Suspended Solids (TSS) is a measure of the amount of particles suspended in the water column and can include a wide variety of material, such as silt, plankton, decaying plant and animal matter, industrial wastes, and sewage. High concentrations of suspended solids can cause many problems for stream health and aquatic life and can block light from reaching submerged vegetation.

Turbidity is the cloudiness or opacity in the appearance of water caused by solids, particles and other pollutants. Turbidity measurements provide an indication of water clarity and water quality.

The water column is an imaginary vertical section of a water body, from the surface to the bottom. Several parameters such as temperature, salinity, nutrient concentrations, PAR, DO, and phytoplankton abundance can change throughout the water column. Scientists use the water column concept to evaluate and monitor the degree of stratification in aquatic environments. 

A watershed is the area of land that drains into a particular body of water. Every body of water has a specific watershed.

Water quality sondes are instruments used to take measurements of various water quality parameters. Sondes are equipped with several sensors for parameters such as temperature, salinity, dissolved oxygen, pH, chlorophyll a, and turbidity. Sondes can be deployed for several weeks at one location to track water quality over time, or they can be lowered through the water column at one location to determine how parameters change with depth at a single time point.

Zooplankton are animals that drift with tides and currents in waterbodies. They eat phytoplankton, and sometimes smaller zooplankton. Zooplankton are important prey for fish, whales, and seabirds. As primary consumers, they are an important link in aquatic food webs.​