The Domino Theory

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The previous information was used to provide a foundation of the general concepts and definitions relating to important freshwater inflow issues.

The difficulty in using flow regimes to manage estuaries is the complexity of estuarine ecosystem functions. One model that can be used to better understand the estuarine relationships is the Domino Theory Model. Although many components are included in the Domino Theory Model, the main relationship that can be shown experimentally is the linkage of bioindicator species, under estuarine resources titled integrity, to the estuarine condition salinity, and then those salinity tolerance ranges to freshwater inflows.

The “Domino Theory” suggests freshwater inflows have an indirect effect. Source: Palmer et al. 2011.

Altered Freshwater Inflows

Studies done in Texas estuaries in the Gulf of Mexico to determine the roles of freshwater inflows found altering the hydrology could cause changes in estuarine systems (Palmer et al. 2011). The inflow studies done to assess the effects of changing flows used benthic invertebrates and macrofauna biomass as bioindicators (Palmer et al. 2008). Bioindicators are species that can be used to signify the health of an ecosystem. Benthic biomass varies by condition. The condition can be defined as the state of ecological resources and the interconnections of ecological resources. Salinity was deemed as the most important ecological condition determining bioindicator species biomass, abundance, and biodiversity. Therefore, these measured changes in bioindicator are correlated with changing freshwater inflows (Kim et al. 2009). Estuarine systems experience changes in many ecosystem components due to altered freshwater inflows including hydro climate, water quality, benthic communities, epibenthic communities, fish communities, invasive species, ecosystem services, and other water resources. Estuarine ecosystem changes have resulted in losses of habitat, biodiversity, and productivity (Montagna et al. 2002b). The use of bioindicators to determine a salinity tolerance range of that bioindicator and then link the salinity range to quantities of freshwater inflows has been integrated and modeled by the Domino Theory as discussed previously and here more in-depth.

Benthic organisms. Source:

Benthic organisms. Source:

Hydrologic Changes of Freshwater Inflow

Hydrologic changes of freshwater inflow into estuaries include those factors that affect the quantity and quality of the inflows. The quantity of freshwater inflows reaching an estuary varies depending on the timing, frequency, duration, and extent of the inflows. The qualities of freshwater inflows vary depending on the inputs into the flows upstream and affect the dynamics of estuaries. Quantity and quality of freshwater inflows can be monitored and related to the resulting changes in salinity levels of the estuary.

        Freshwater inflow quantity

The quantity of freshwater inflow depend on the frequency, duration, and extent of flow-producing rain events. This section describes the sources affecting the amount of freshwater inflows into the estuary. It also describes how the freshwater inflows change.

  Timing of freshwater inflow events:

Climatic events and anthropogenic impacts cause variations in the timing freshwater inflow events occur. The timing of freshwater inflows is important for many organisms within the estuarine system.  For example, many species use salinity change as a cue for changes in the stages of the organism’s life cycle (Montagna 2013). Understanding the influence of variations in freshwater inflows is a key component causing change in estuarine systems, and thus is important for the management of freshwater inflows.

                        Climatic Influences on timing of freshwater inflow

Climate is the average weather pattern that occurs in a particular area. Weather is the short-term variations and conditions of temperature, humidity, precipitation, atmospheric pressure, and wind (Montagna et al. 2013). As you move from the equator towards the poles, either the Arctic or Antarctic, temperature, precipitation, and humidity generally decrease (Montagna et al. 2013).

The world’s major communities including the dominant vegetation, species and climatic conditions are referred to as biomes. Biomes vary depending on the geographic location and can be categorized by climatic features such as the relationship between precipitation and temperature, and whether the biome is aquatic or terrestrial. Some terrestrial biomes include desert, tropical rainforest, tropical savannah, Mediterranean, and tundra. Some aquatic biomes include wetlands, estuaries, oceanic abyssal, and ocean pelagic.

Aquatic Biomes. Source:

Aquatic Biomes. Source:

A biome has characteristic seasonal patterns, which makes knowing the biome of an estuary’s watershed important for the timing of freshwater inflows. For example, in southwest Texas, the dominant biome is grassland/shrublands, and the climate is mainly semi-arid. The seasonal cycle is a dry winter, rain in the spring, and hot summers. Grasses and shrubs on rolling plains characterize the vegetation although agriculture has significantly altered this historically dominant vegetation. Here, the timing of significant freshwater inflows occur in the spring or fall due to precipitation. The freshwater inflows can flush excess organic material and mix lush nutrients into the estuarine system. In Texas, hot and dry summers can cause estuaries to become still and stagnate leading to high temperatures and low oxygen content in the water. In northern North American estuaries, snowmelt in the spring plays a large role in contributing freshwater inflows to the estuaries.

Snow melt. Source: (Andrusdevelopment)

Snow melt. Source: (Andrusdevelopment)

Coastal storm, especially hurricanes can reallocate sand, sediment, and mud, tear up shorelines and vegetation. Storm winds can create violent currents that damage habitats and push saltwater upriver. Other storm events like floods reduce salinity levels while droughts can result in higher salinity.

Sea level rise also poses a threat to the World’s estuaries. Global climate is warming at an accelerated rate, causing polar glacier to melt (IPCC 2013). Glacial melt increases the water in the World’s oceans. A warmer ocean also will experience thermal expansion, which will lead to higher sea levels (IPCC 2013). The increase of sea-level rise in the oceans causes an encroachment upon the coastal wetlands and is referred to an inundation (IPCC 2013).

                         Upstream Modifications effect on timing of freshwater inflow events

The natural timing of freshwater delivery to an estuary may be altered by upstream modifications created by humans. Dams that are created to control flooding can result in reduced seasonal variation of freshwater inflows (Montagna et al. 2013). Urbanization and construction projects change runoff patterns as previously discussed. This can increase the volume of freshwater inflows but shorten the delivery time to estuaries.

                        Timing of freshwater inflow events impact on estuarine resource

Climatic and anthropogenic influences may alter the timing of the delivery of freshwater inflows to estuaries and impact estuarine resources by changing salinity levels. Estuaries are negatively affected by a decrease in quantity of spring freshwater inflows.

Life cycle cues of various fish and shellfish are signaled to high spring runoff occurrences causing alterations in timing that impact spawning and nursery cycles (Alber 2002). For example, a study done in Sabine Lake, Texas on the effects of building a dam found the dam affected inflow patterns by reducing the availability of both low salinity nursery habitat for brown shrimp in the spring and high salinity nursery habitat for white shrimp in the summer (White and Perret 1974, referenced in Alber et al 2002). Altering the timing of freshwater inflows changes salinity levels over time in estuaries. Organisms’ response to salinity change is complex and varies depending on a species’ salinity tolerance range.

                Frequency of freshwater inflow events

The frequency of significant freshwater inflow events alters the quantity estuaries receive. Long periods of little of no freshwater inflow events into estuaries have been shown to negatively affect benthos diversity, abundance, and biomass (Palmer et al. 2008). Salinity will continue to increase with decreased freshwater inputs because evaporation processes continues over the estuary.

                Duration of freshwater inflow events

The duration of time that freshwater flows into estuaries differs with quantity of flows and the size of the river and estuary. Construction of roads increases the amount of impervious surface area. Surface runoff flows much more quickly over impervious surfaces than riparian surfaces. These surfaces also help humans intercept the water in storm drains before it reaches an estuary. The surface water that does reach a creek, stream or river does so at an accelerated pace. The freshwater inflows that estuaries do receive may come less frequent and at much larger volumes. The sudden change in salinity consequently negatively affects the estuarine flora and fauna.

                Mixing Rate of freshwater inflow events

Freshwater inflows mix with saltwater from estuaries. The rate of mixing depends on the volume, the salinity, and the tidal action of the estuary and the amount of freshwater. Decreases in freshwater inflow cause changes in the extent of the mixing area of the estuary and greater stratification. Stratification occurs when fresh water rises above the saltwater and creates a salt wedge. Decreases in freshwater inflows can also cause the salt water to move upstream. This shifting affects the distribution of both rooted vegetation and sessile organisms. One example of species changing distribution with decreased freshwater inflow is the upstream movement Spartina, a common cordgrass species that has been linked to long term increases in salinity in both Delaware River and Chesapeake Bay (Schuyler et al. 1993; Perry and Hershner 1999). Upstream movement of saltwater can alter intertidal habitats that normally exist under low salinity conditions. Benthic organisms that move upstream with the saltwater may be introduced to unfavorable new conditions (Alber et al. inflowpdf). Other studies have linked changes in river flow to changes in migration patterns, spawning habitat, and fish recruitment (Drink water and Frank, referenced in Alber et al.).

        Freshwater Inflow Quality

The quality of freshwater inflow changes the distribution of nutrients, sediments, organisms, and organic material in an estuary. Estuarine alterations have possible consequences that alter ecosystem dynamics and productivity (Alber and Merryl 2002). Freshwater inflow is usually positively correlated with sediments and nutrients including nitrogen.

Freshwater inflow can enhance nutrients and increase primary production in estuaries (Palmer et al. 2002). The often-large nutrient concentrations freshwater inflows carry into estuaries has been correlated with nitrogen loading and phytoplankton production (Flint et al. 1986; Nixon 1992; Mallin et al. 1993; Boynton et al. 1995, referenced in Alber et al.). In a study done on restored freshwater inflows to Nueces Delta, Texas, Polychaete S. benedicti rapidly increased following a freshwater event (Palmer et al. 2002). This primary production is a food source that can be consumed by bivalves or deposited onto sediment surfaces where it may be consumed by interface feeders such as polychaetes and crustaceans. The relationship between inflows and secondary production is difficult to determine due to the complexity of trophic structures but increased nutrient inflow is generally positively correlated with increases in secondary production (Alber et al.).

               Measuring water quality parameters

Water quality parameters can be measured using a water quality sonde tool. Sondes can measure multiple parameters at the same time including salinity, ph, dissolved oxygen, conductivity, temperature, nitrate, ammonium, and more depending on the brand of sonde. An example of a sonde is shown below.


Estuarine Condition


Estuarine condition is the saline and tidal conditions occurring due to tidal action and mixing of fresh and salt water in the estuary. When referring to estuarine condition, we are referring to the salinity, sediment, dissolved material, and particulate material of the estuary. In a laboratory, water is often purified to remove all other materials, containing only oxygen and hydrogen atoms. This water is called distilled water. Distilled water does not normally occur in the real world. Water is often diluted with salt, organic, and particulate material. This material can either benefit or cause negative effects in an estuary.


Water in an estuary has dissolved salt within it. The salinity gradient generally increases from the input source of an estuary, usually a stream or river, to the output source, the sea or ocean. Salinity is measured in gravimetrically as parts per thousand of solids in liquid or ppt.  The salinity of the ocean is generally around 35 ppt (Antonov 2006). Another salinity unit is the practical salinity unit or PSU measurement, which is based on water temperature and conductivity measurements made by sondes and the ocean is also generally around 35 PSU (Antonov 2006). Using ppt or PSU gives similar results for the ocean’s seawater salt content (Antonov 2006).

The fresh water from rivers has salinity levels of 0.5 ppt or less. Within the estuary, salinity levels are referred to as oligohaline (0.5-5.0 ppt), mesohaline (5.0-18.0 ppt), or polyhaline (18.0 to 30.0 ppt) (Montagna et al. 2013). Near the connection with the open sea, estuarine waters may be euhaline, where salinity levels are the same as the ocean at more than 30.0 ppt (Mitsch and Gosselink 1986). An example of this is shown in the illustration below:

The salinity of an estuary can vary dependent on the amount of freshwater inflows as well as the tidal movement and location within the estuary. Estuaries have a water balance that is either positive, freshwater inputs exceed evaporation; neutral, there is a balance between freshwater inflows and evaporation; or negative, freshwater inflows are less than the amount of evaporation (Montagna et al. 2013).

Seasonally in the U.S., estuaries generally decrease in salinity in the spring months with increased inflows making the system a positive estuarine system. In the summer, estuaries increase in salinity with decreased freshwater inflows and increased evaporation due to higher temperatures causing the system to be classified as a negative estuarine system.

Salinity affects the chemical conditions within an estuary, most notably the amount of dissolved oxygen. Solubility is the amount of oxygen that can dissolve in water, which decreases as salinity increases. Solubility is important because estuarine organisms have salinity ranges they can tolerate before they experience stress (Montagna et al. 2013). Some estuarine species can adapt to changes oxygen levels by practicing avoidance techniques. Fish can swim away to areas with tolerable salinity levels. Other organisms such as mollusks, oysters, and benthic organisms cannot travel large distances. Salinity levels outside of their tolerance ranges cause negative affects including increased stress and decreased reproduction and survival rates (Palmer et al. 2008).

                        Salinity characteristic types in estuaries

As discussed earlier, the characteristic types of salinity distributions in estuaries often depend on the driving force that mixes the estuary and includes: salt-wedge, partially mixed, well mixed, and inverse.

                        An estuarine system can be classified by the salinity zone

When river flow drives mixing in estuaries and where tidal currents and waves are not strong enough to mix the water column, the freshwater flows over seawater causing stratification and is categorized as a salt-wedge estuary (Montagna et al. 2013). A partially mixed estuary is when tides drive the mixing in a partially mixed estuary causing some stratification of bottom saltwater and top freshwater with gradient variation at different areas of the estuary (Montagna et al. 2013). A well-mixed estuary is when wind drives the mixing in a well-mixed estuary and there is a salinity gradient that increases from the river to the estuary (Montagna et al. 2013).  Inverse estuaries occur when evaporation exceeds the amount of freshwater inflows leading to hyper-saline conditions (Montagna et al. 2013). The water in the estuary becomes dense with salt and sinks to the bottom. The less dense seawater flows into the estuary from the sea or ocean on top of this layer. An estuary can take any of these salinity zones depending on the time of year and location of the estuary.

                Importance of salinity

Water development projects can reduce the capacity of the land to deliver freshwater to estuaries and change timing and frequency of freshwater pulses, in turn affect estuarine organisms adapted to historic saline conditions.

Salinity is an important indicator of estuarine condition. Remember, when trying to determine flow standards, an indicator species can be used to determine that organism’s salinity tolerance range (Montagna et al. 2013). The biological indicator’s salinity tolerance range has the capacity translate to acceptable salinity levels within the estuary. The acceptable salinity range in the estuary could be created with freshwater inflows by determining the mixing rate, or how much freshwater is necessary to mix with the volume of saltwater within the estuary to result in the desired salinity range (TCEQ 2009).

       Particulate Material

Freshwater inflows carry sediments, nutrients, and organic materials into estuaries providing necessary components to maintain productivity and habitats of estuarine ecosystems (Montagna et al. 2002). The estuary is protected from strong tidal action and currents due to offshore peninsula and barrier islands, created by sediments settling out and forming banks. The sediments also support beaches and provision the inter-tidal wetlands. Particulate matter delivered to estuaries by freshwater inflows the primary energy source for organisms living in the estuary (Day et al. 1989). The timing of conveyance of sediments, nutrients, and organic material is affected by changes upstream (Montagna et al. 2013). Upstream diversions of freshwater are decreasing the amount of freshwater inflows that carry water, sediment, nutrients, and organic material to the estuaries.

Dams are a source of upstream diversions, affecting the water quality of freshwater inflows by catching sediment and reducing the downstream delivery of particulate materials (Alber 2002). The catchment of particulate material behind dams can lead to lag times in its release to the estuary disrupting the quality and accessibility of organic material (Vorosmarty and Sahagian 2000).

Other upstream changes affecting the loading of sediment, nutrients, and organic material include both point and non-point sources. Non-point sources are difficult to determine because the pollutants that result from them are wide spread and disperse. Some examples of non-point source discharges include agricultural runoff, gas and pipe leaks, salt from irrigation practices, and sediment from construction projects. The sources of point source discharges are more distinct and identifiable. Some examples of point source discharges include discharges from wastewater treatment facilities, industrial plant’s discharges, and sewer outfalls. Both point and non-point sources affect downstream water quality including nutrient and sediment concentrations and when combined with changes in freshwater inflow delivery times, can greatly alter loading patterns to an estuary. (Albers 2002)


In estuaries, primary producers take up nutrients such as nitrogen and phosphorus (D’Elia 1986). Therefore the growth of phytoplankton is correlated with a depletion of nutrients in estuaries. Freshwater inflows carry nutrients into estuaries, replenishing the stock for phytoplankton use (D’Elia 1986). The sources of many of the nutrients are from human activities including sewage inputs and agricultural runoff.

Annual variations in delivery of nutrient to the estuary by freshwater inflows are primarily due to annual rain and snowfall (TWDB 2012). Human activities have altered the concentrations and timing of nutrients like nitrogen and phosphorus. The changes in nutrient concentration have implications for the species dynamic of the estuary (D’Elia 1986). The species composition of algae may change to favor species, such as toxic algae, having negative affects on human and aquatic species, such as oysters, health (USEPA 2013).


The EPA has developed nutrient pollution outreach and education materials for the public that can be found online at:

Estuarine Resources

Estuaries are important coastal areas, providing many natural resources for humans. A natural resource is any entity or process that contributes positively to humans. Some examples of estuarine resources include fish, shellfish, mollusks, crabs, benthos, seagrass beds, oyster reefs, and many other organisms. Some benefits provided by estuaries and their resources include pollutant filtration, nursery areas, protection from storm events, and much more.

It is important for an estuary’s resources to maintain a good integrity and functionality in order to be considered sustainable resources (Alber 2002). The integrity of an estuarine resource can be evaluated by understanding the species’ composition, biomass, abundance and diversity (Alber 2002). The functionality of estuarine resources includes the primary production, secondary production, and nutrient recycling (Alber 2002). Sustainability is the condition in which estuarine resources continue to carry out life functions and processes. The stability of the estuary relies on the persistance of habitats, valued resources, and ecosystem services.


The use of benthic organisms to indicate ecological integrity is beneficial for several reasons. Benthos are indicators of many environmental stressors because they are able to integrate spatial and temporal changes in ecosystem factors (Smith et al. 2001). Another rational for using benthos is that they cannot travel large distances when ecosystem condition change. This is important because abundance, diversity, and biomass changes can be measured over long periods of time at established sampling points and more accurately reflect the changes in ecosystem condition. Other marine organisms such as fish are more mobile and changes in biomass, diversity, and abundance can be the result of other biological responses including avoidance.

For the domino theory, the species used to determine the ideal freshwater inflow regime for a given estuarine system that will restore or maintain a sustainable estuary are that estuary’s benthos. Benthos are ideal indicator species for many reasons, namely their ability to reflect changes in salinity. Although benthos have a wide salinity range, they often only function within a minute range (Montagna et al. 2013). Table 4 shows the salinity tolerance range of several estuarine system indicator species.

Benthos samples are taken using cores. Cores are tubes that take replicate samples at each study site at the surface of the bottom substrate and are then taken back to the lab where the substrate is removed and benthic organisms can then be studied to determine species composition, abundance, biomass and diversity. Replicates are multiple samples from the same location at the same time to increase confidence in data measurements.

Changes in benthos are determined by measures of their status and are referred to as indices. Therefore, qualifying and quantifying a species using indices can be used to determine the integrity of estuarine resources. For the purpose of understanding the relationship of freshwater inflows with the estuary, and as discussed earlier, indices that are studied here are of the indicator species of interest. The quantifiable indices include the indicator species composition, abundance, biomass, and diversity. In this way, indicator species indices can provide a measure of ecological changes in the environment.  Salinity effects on selected estuarine macrobenthic and epibenthic organisms.

Salinity tolerance of estuarine system indicator species. Source: Montagna et al. 2013

Authors Organism(s) Studied Study Location Salinity Tolerance Results
Chadwick & Feminella (2001) Burrowing mayfly Hexagenia limbata USA (Alabama) Laboratory bioassays showed that H. limbata nymphs could survive elevated salinities (LC50 of 6.3 ppt at 18 C, 2.4 ppt at 28 C).  Similar growth rates at 0,2,4, & 8 ppt.
Saoud & Davis (2003) Juvenile brown shrimp Farfantepenaeus aztecus USA (Alabama) Growth significantly higher at salinities of 8 & 12 ppt than at salinities of 2 and 4 ppt.
Tolley et al. (2006) Oyster reef communities of decapod crustaceans & fish USA (Florida) Upper stations (~20 ppt) and stations near high-flow tributaries (6-12 m3 s-1) were typified by decapod Eurypanopeus depressus & gobiid fishes. Downstream stations (~30 ppt) and stations near low-flow tributaries (0.2-2 m3 s-1) were typified by decapods E
Montagna et al. (2008a) Southwest Florida mollusc communities USA (Florida) Corbicula fluminea, Rangia cuneata, & Neritina usnea only species to occur < 1 psu.  R. cuneata good indicator of mesohaline salinity zones with tolerence to 20 psu.  Gastropod N. usnea common in fresh to brackish salinities.  Polymesoda caroliniana prese
Montague & Ley (1993) Submersed vegetation & benthic animals USA (Florida) Mean salinity ranged from ~11-31 ppt.  Standard deviation of salinity was best environmental correlate of mean plant biomass and benthic animal diversity. Less biota at stations with greater fluctuations in salinity.  For every 3 ppt increase in standard
Rozas et al. (2005) Estuarine macrobenthic community USA (Louisiana) Increased density and biomass with increases in freshwater inflow and reduced salinities.  Salinity ranged from 1-13 psu.
Finney (1979) Harpacticoid copepods Tigriopus japonicus, Tachidius brevicornis, Tisbe sp. USA (Maryland) All species tested for response to salinities from 0-210 ppt.  Tigriopus became dormant at 90 ppt died at 150 ppt.  Tachidius became dormant at 60 ppt, died at 150 ppt.  Tisbe died shortly after exposure to 45 ppt.
Kalke & Montagna (1991) Estuarine macrobenthic community USA (Texas) Chironomid larvae & polychaete Hobsonia florida: increased densities after freshwater inflow event (1-5 ppt).  Mollusks Mulinia lateralis & Macoma mitchelli: increased densities & abundance during low flow event (~20 ppt).  Streblospio benedicti & Medioma
Keiser & Aldrich (1973) Postlarval brown shrimp Penaeus aztecus USA (Texas) Shrimp selected for salinities between 5-20 ppt.
Montagna et al. (2002b) Estuarine macrobenthic community USA (Texas) Macrofauna increased abundances, biomass & diversity with increased inflow; decreased during hypersaline conditions.  Macrofaunal biomass & diversity had nonlinear bell-shaped relationship with salinity: maximum biomass at ~19 ppt
Zein-Eldin (1963) Postlarval brown shrimp Penaeus aztecus USA (Texas) In laboratory experiments with temperatures 24.5-26.0 C, postlarvae grew equally well in salinities of 2-40 ppt.
Zein-Eldin & Aldrich (1965) Postlarval brown shrimp Penaeus aztecus USA (Texas) In laboratory experiments with temperatures < 15 C, postlarval survivial decreased in salinities < 5 ppt.
Allan et al. (2006) Caridean shrimp Palaemon peringueyi South Africa At constant salinity of 35 ppt, respiration rate increased with increased temperature.  At constant temperature of 15 C, respiration rate increased with increased salinity.
Ferraris et al. (1994) Snapping shrimp Alpheus viridari, Polychaete Terebellides parva, sipunculan Golfingia cylindrata Belize Organisms subjected to acute, repeated exposure to 25, 35, or 45 ppt.  A. viridari hyperosmotic conformer at decreased salinity, but osmoconformer at increased saliniry.  G. cylindrata always osmoconformer.  T. parva always osmoconformer; decreased surviv
Lercari et al. (2002) Sandy beach macrobenthic community Uruguay Abundance, biomass, species richness, diversity & evenness significantly increased from salinity of ~6 ppt to salinity of ~25 ppt.
Chollett & Bone (2007) Estuarine macrobenthic community Venezuela Immediately after heavy rainfall (~25 psu), spionid polychaetes showed large increases in density & richness versus normal values (~41 psu).
Dahms (1990) Harpacticoid copepod Paramphiascella fulvofasciata Germany (Helgoland) After 2 hours, no mortality in salinities of 25-55 ppt.  Almost all displayed dormant behavior < 20 ppt and > 55 ppt.
McLeod & Wing (2008) Bivalves Austrovenus stutchburyi & Paphies australis New Zealand Sustained exposure (> 30 d) to salinity < 10 ppt significantly decreased survivorship.
Rutger & Wing (2006) Esturaine macroinfaunal community New Zealand Infaunal community in low salinity regions (2-4 ppt) showed low species richness & abundance of bivalves, decapods, & Orbiniid polychaetes, but high abundance of amphipods & Nereid polychaetes compared to higher salinity regions (12-32 ppt).
Drake et al. (2002) Estuarine macrobenthic community Spain Species richness, abundance, and biomass decreased in the upstream direction, positively correlated with salinity. Highly significant spatial variation in macrofaunal communities along the salinity gradient. Salinity range: 0-40 ppt.
Normant & Lamprecht (2006) Benthic amphipod Gammarus oceanicus Baltic Sea Low salinity basin (5-7 psu).  Physiological performance examined from 5-30 psu.  Feeding & metabolic rates decreased with increasing salinity; nutritive absorption increased.  Feces production & ammonia excretion rates decreased strongly from lowest to

                        Species composition

Species composition is the number of taxonomic species in a given area and how well each of those species is represented in that area by the number of individuals in its population. The species composition of one area can be compared to other areas. Studies done on species composition over time can help determine ecological changes in each study area.

In regards to freshwater inflows, the chosen indicators’ species composition is often studied before during and after a freshwater inflow event at study sites close to the mouth of the estuary to study sites further away. The species composition over time can indicate how the freshwater inflow events affect the community composition or structure.

                                Species abundance

Species abundance is simply some measure of the species in a sample. The species abundance of an area or of an entire estuary reflects the salinity of the estuary at the time the species samples were taken. In this way, it is representative of the species’ salinity tolerance. Some measure of the species abundance includes density, biomass, territorial area and the number of breeding pairs.


The biomass is the mass of the living or once living matter within a given environmental area. Biomass can be measured for both animal and vegetable derived material. Biomass is structured from a carbon base and composed of a mixture of organic molecules.


Species diversity measures the diversity within an ecological community by incorporating the two concepts of species richness and species’ abundances. A community with a greater number of species indicates greater diversity, so long as each species is similarly represented by species composition.


Further information on species integrity visit:

        Estuarine Resources Function

Estuaries are some of the most productive areas on Earth. Many species rely on estuaries for their survival. They provide feeding grounds, nursery habitats, and breeding grounds. Humans also depend on estuaries for recreational use, food, and job opportunities.

Some 22 of the 32 largest cities in the world are located on estuaries (Ross 1995). Human activities are causing greater degradation of estuaries and their resources, making them amongst the most threatened ecosystems on Earth (NOAA 2013). The degradation of estuaries reduces the ability of the ecosystem to carry out many functions.

The functioning of estuarine resources include the distributions and abundances of estuarine biota based on how they interact and respond to estuarine conditions and the consequences of those interactions on community structure, food web interactions, rate of primary and secondary production, and material cycling (Alber 2002). Changes in estuarine resources’ functioning occur primarily from changes in freshwater inflows.

Salinity determines the habitat dynamics and in turn the distributions of organisms. This is because differing freshwater inflows in an estuary cause shifting isohalines that affect the vegetation and organism allocation (Alber 2002). The effect of changing locations of intertidal habitats caused by shifting isohalines can lead to implications on the suitability of the new location for benthic organisms. Changes in spatial distribution of critical habitat are therefore important to evaluating changes in freshwater inflows (Sklar and Browder 1998; Alber 2002).

As discussed earlier, although most of the estuarine organisms have a wide range of salinity tolerance, most occur within a focused salinity range depending on the organism’s life history stages. Organisms capable of horizontal and vertical movement such as blue crabs and fish species are also affected by changes in the estuarine salinity structure. Changes in species composition, distribution, abundance, and survival of estuarine organisms are linked to freshwater inflows (Montagna et al. 2013). Also linked to freshwater inflows are migration patterns, spawning habitats, and fish recruitment (Drinkwater and Frank 1994: referenced in Alber 2002).

The timing of freshwater inflows is important for estuarine resources because the delivery of freshwater flows triggers cues in the life histories of many organisms. For instance, shellfish and fish are cued to high spring inflows but changes in inflows can affect spawning and nursery cycles (Alber 2002). In Texas, a study done on the impact of salinity variability on estuarine organisms, a negative correlation was found between the standard deviation of salinity and the density of benthos that showed frequent salinity fluctuations lead to increases in physiological stress (Montagna and Kalke 1992).

The impacts of changes in freshwater inflows and the sediment, organic matter, and nutrients carried in the flows due to upstream activity can affect primary production, secondary production, nutrient cycling and the trophic structures in the estuary (Alber 2002). The relationship between freshwater inflows is a complex and dynamic one, with different trophic levels consequently affecting the other. Next, a brief overview of the trophic system will be given and information regarding primary, secondary, and nutrient cycling will be provided.

               Trophic structure

Tropic structure is a tiered structure of the organism in an ecosystem, with each level representing those organisms that share a similar function and food source. Trophic structure diagrams also depict the energy transfer from on trophic level to the next. By organizing the estuary into a trophic structure, we are given an indication of the productivity of the estuary. Productivity is basically the ability of the estuary to yield organic matter. A productive estuary is one that has high diversity, high survival rates, little to no invasive species, and whose organisms continually carry out life processes; in other words, the estuary is sustainable. Freshwater inflows are fundamentally linked to estuarine productivity.

An example of a trophic structure is shown below. This trophic structure looks at the aquatic ecosystem from a bottom up point of view. The bottom tier organisms, or primary producers, are the most energy efficient, while the top tier, or top predators, are the least energy efficient. Primary producers produce their own food, making them more energy efficient, while top fish or predators require many organisms, making them less energy efficient. Another way to say this is that predators have a much higher energy demand than do phytoplankton. The trophic structure in Figure 10 below shows an ecosystem functioning by interrelationships and life processes. Freshwater inflows balance the estuaries by providing hydrological requirements for the organisms.

                Primary Production

Primary producers largely contribute to making estuaries some of the most productive ecosystems on the Earth. There is generally greater productivity near the coasts than in the open ocean. Coastal areas are hotspots for primary producers who require higher sunlight conditions, nutrient sediment, and organic inputs, and protection from large tidal events in order to be productive.

Primary production is the production of organic material from aquatic or atmospheric carbon dioxide through either photosynthesis where light is the source of energy or chemosynthesis, which uses the oxidation, or reduction of chemical compounds as the energy source. To carry out photosynthesis or chemosynthesis some necessities include energy from the sun, carbon dioxide, and nutrients such as nitrogen and phosphorus.

A source of nutrients for primary producers in an estuary is from freshwater inflow. Many studies have found a correlation between nitrogen loading and phytoplankton productivity (Flint et al. 1986; Nixon 1992; Mallin et al.1993; Boynton et al. 1995; referenced in Alber 2002). Solis and Powell (1999) studied 5 Texas estuaries and found a positive correlation between fish harvested and nitrogen loads (Alber 2002). The opposite is true that decreased freshwater inflows are correlated to decreased rates of primary and secondary production (Drinkwater and Frank 1994).

Human activity can increase the amount of nutrient inputs and increase the speed of inflow pulses, negatively affecting estuarine ecosystem primary production. Increased nutrients in the system, or nutrient loading, and high pulse inflow events lead to decreased light penetration from turbidity and reduced flushing time, reducing the ability of phytoplankton to photosynthesize and grow (Alber 2002).

                Secondary Production

Secondary production is the rate of incorporation of biomass by heterotrophic, or consumers, organisms through consumption of organic material and/or primary producers. The process is driven by transference of organic material between different trophic levels.

The role of freshwater inflows and secondary production is often difficult to decipher. It is commonly accepted that organic material input is important for secondary and primary producers alike. One example is the existence of an upstream dam on the Mbashi estuary in South Africa caused a reduction in the input of silt and detritus, or non-living organic matter that was linked with a decrease in fish abundance (Plumstead 1990). There is also isotope evidence land-derived organic material is important to estuarine bivalves (Day et al. 1994). In many systems, increased inflows led to increased fish and shellfish catches (Alber 2002).

                Nutrient Cycling

Nutrient cycling in an estuarine ecosystem is the referral of organic and inorganic matter into an estuary and their transference into the production of living matter. These nutrients must maintain a balanced concentration in order to create a sustainable estuary. A conceptual model showing the nutrient cycle is shown below.

Primary and secondary consumers, particularly benthic organisms play a large role in the regulation of nutrient concentrations and consequently the productivity in estuarine systems (Nixon 1981). Sediments, which are permanently or principally inhabited by macrofauna, can be a source or a sink for nutrients (Nixon 1981). A sink in an estuary occurs when substances or forms of energy are absorbed and therefore removed from the water cycle. Several studies have shown the life activities of macrofauna including eating, burrowing, and excretion of wastes can influence the interchange of matter between the sediment and the above water column (Aller 1979, 1982; Kristensen et al., 1985, 1991; Hansen and Kristensen, 1997; Riefel et al. 1997; referenced in Pennifold and Davis 2001).  One study found that benthic macrofauna do indeed contribute largely to the nutrient cycling in their study of the Swan-Canning Estuary (Pennifold and Davis 2001).

Climate change can impact the ability of the estuary to carry out nutrient cycling processes. A combination of several or all factors including increased temperature, reduced inflows, increased inflow pulses, and nutrient fluxes can create anoxic conditions, which occur when oxygen is depleted from the estuarine system. Anoxic events may alter the nutrient cycle by interrupting macrobenthic activities that can influence the nutrient cycle and transformations. (Pannifold and Davis 2001)

Anthropogenic influences can greatly affect the nutrient cycling processes of estuarine organisms through the increased introduction of waste discharges. The effects on organisms occur not only at the community level, but responses to anthropogenic wastes can be measured at the population, organismic, cellular and subcellular levels of organization (Kennish 1991). Rapid assimilation of heavy metals from water, food, and/or sediments has been shown for phytoplankton, zooplankton, and macroalgae (Kennish 1991). Macrobenthic invertebrates and mollusks eliminate heavy metals at a slow rate and are a source of bioaccumulation (Kennish 1991). Bioaccumulation is the accumulation of wastes and other substances via the organismal tissue. Disruption of the nutrient cycle can cause a decline in estuarine health and productivity.  Biomagnification is the accumulation of substances via trophic links.

Estuarine Resources Sustainability

Estuarine ecosystems are among the most productive ecosystems on the planet. Marine habitats are valued at providing an estimated $14 trillion worth of ecosystem goods and services annually, or 43% of the global total (Costanza et al. 1997). Scientific evidence in the face of anthropogenic global change is showing many of these marine ecosystems are threatened (IPCC 2001).

Sustainability includes the valued habitats, resources, and ecosystem services provided. It is important to look at freshwater management in terms of sustainability at these levels to determine what resources can be protected, the important habitats for their survival, and the economic importance of those resources.

Economists work with scientists to study how humans apportion natural resources based on their wants by valuing natural resources and processes. Ecosystem services are any resource or organisms that occur in a natural state and/or organism’s life processes that can be used for monetary gain; this includes freshwater. Economists and scientists can work together to provide tools that address the issues of balancing growth with conservation of natural resources.

                Key Habitats

While unconsolidated sediments are the most common habitat in estuaries, several habitats are key to the high productivity characteristic of an estuary. These habitat types include mangroves, saltmarshes, oyster reefs, and seagrass beds. All habitats support estuarine biodiversity and provide many organisms with nursery grounds, feeding areas, and tidal and predator protection. Some habitats such as mangroves anchor the sediment to help prevent sediment erosion and displacement.

                        Unconsolidated sediment

Unconsolidated sediments are estuarine habitats with little to no vegetation and sediments smaller than pebbles. Area of the estuary where unconsolidated sediments occur can be hydologically classified as subtidal, permanently flooded, semipermanently flooded, and/or intermittently exposed. The composition and distribution of organisms is determined by the habitat’s exposure to wave and current action, temperature, salinity, and light penetration. Because there is little to no vegetative protection, most inhabitants are macroinvertebrates within the substrate.

                        Seagrass beds

Seagrasses are flowering plants that are located in the subtidal zone of estuarine systems submerged in estuarine waters except for occasions when low tides expose seagrass to the air (NOAA 2004). Seagrasses appear similar to blades of grass, although they are not part of the grass family (NOAA 2004). Seagrass habitats occur where water clarity is high because the photosynthetic plants require high levels of sunlight. Seagass beds provide many services to the ecosystems including maintaining water clarity by capturing particulate matter in the water column with their leaves, providing shelter for fish, shellfish, and crustaceans, using their roots to stabilize bottom sediment, and providing a food source for many estuarine organisms as well as watering birds.


Mangroves are trees or shrubs that grow in the intertidal zone of estuaries and provide erosion protection, storm damage, and tidal action (NOAA 2004). The mangrove’s roots and leaves filter sand and other material. Mangroves also provide shelter, food, nursery habitats, and protection for many fish species, crabs, shrimp, mollusks, sea turtles, manatees, and bird species. Mangroves have the ability to adjust to changing tides, temperature, ocean currents, and various soil types including mud, sand, coral, rock and peat (NOAA 2004).


A salt marsh is a marshy area occurring at the upstream portion of the estuary. Saltmarshes in estuaries are areas of high productivity and biodiversity. Food is supplied to marsh species through the decomposition of saltmarsh vegetation and other salt marsh organisms. Bacteria and algae aid in the decomposition of detritus, or dead and decaying, material resulting from marsh plants. Fish, crabs, shrimp, and worms eat the detritus material. The microorganisms then consume the feces of the fish, crabs, shrimp, and worms. Materials not taken-up by marsh inhabitants, act as fertilizer for the next generation of marsh plants. Salt marshes also provide protection from predators and nursery habitats for fish, turtles, bird species, and other organisms.









                        Oyster reefs



Oyster reef habitats provide young, free-floating larval oysters with a substrate to settle on, protection of young mollusk, crab, and fish species, and water filtration. Oyster prevent algal blooms by filter feed on algae that can reduce the water quality and also inadvertently remove pollutants and other matter that may be harmful to estuarine health. Estuaries that experience excess nutrient loading can have algae populations explode in the upper water column until little nutrients are left and the population then crashes, leaving decaying organic matter in the water and creating hypoxic condition. Hypoxic conditions indicate an unhealthy estuarine system and are characterized by low oxygen levels and low visibility. Oyster reefs provide a means of preventing algal blooms, insurance of future oyster generations, and protection of many organisms.

Today, only an estimated 15% of oyster reefs remain worldwide, making them among the most threatened marine habitats (Pollack 2012). Oyster reef habitats are constantly at risk of being destroyed or removed from anthropogenic activities, water quality degradation, climatic events, and pollution events (Pollack 2012). Oyster reef restoration and protection efforts in the Gulf of Mexico may provide a way to bring back the oyster reef habitats. The figure below shows oyster removals for anthropogenic use along the Atlantic and Gulf of Mexico coast are still occurring, showing oyster populations in these waters are still present.

Source: Pollack 2012.


Oyster sentinel monitors the health of estuaries in the Gulf of Mexico by conducting studies using eastern oysters. The Oyster sentinel can be found online at:

                Ecosystem Services

Ecosystem services are the goods and services provided by an ecosystem that translate into benefits for people. Some examples of ecosystem services include nutrient cycling, flood control, water filtration, and habitat for plants and animals. Understanding how anthropogenic activities impact the ecosystem by valuing the ecosystem goods and services give information on how valuable the ecosystem is.

Ecosystem services integrate ecological economics and best available natural science. Ecosystem services provide a way to look at ecosystem functions in an economic context. An example of this would be putting a price on how much water is filtered by riparian plants a day by calculating the cost of filtering that same amount of water using a wastewater treatment plant.


Further information on ecosystem services can be found through online publications:

Ecosystem Services as a Common Language for Coastal Ecosystem-Based Management:

Obscuring Ecosystem Function with Application of the Ecosystem Services Concept:

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One comment

  1. I appreciate this information. I can use it for the water curriculum at our Maine Environmental Science Academy at Molly Ockett Middle School-Fryeburg ,Maine .

    In Maine, I can estimate that the timing and quantity of freshwater flows has been altered significantly
    in the last 45 years. I estimate that estuarine inflow in larger rivers has been reduced by 40 percent on average in the spring ,summer and fall and increased in the late fall and winter. One reason is hydro generation but the main reason is lake association political power to keep lakes at full pond for boating access and dock accessibility. Bass fishing grou7ps are allied with the lake associations. Sebago Lake is a prime example of this unnatural management. Scientific study of altered flow impacts are greatly needed here in Maine. Also, attention is needed on changes in silica delivery to the ocean.
    Since the 1970′s It seems that HAB occurrence( duration, frequency, and intensity) increased when freshwater flow changes started about the same time period. The severity has increased and I would bet it is somewhat linear with increased reduction in freshwater flow if variability in precipitation and ocean currents changes are excluded.
    Not enough dissolved silica—– fewer diatoms——reduced suppression of HABs -reduced coastal productivity. Great example of Domino Theory.

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