Recent anthropogenic activities have caused a significant change in the turbidity of freshwater and marine ecosystems (Kapsimalis et al., 2014). Understanding the mechanisms through which species interactions are influenced by anthropogenic change has come to the lead of many ecological disciplines. Turbidity is essentially a measurement of how cloudy or clear the water is, or, in other words, how easily light can be transmitted through it. Turbidity affects organisms that are directly dependent on light, like aquatic plants, because it limits their ability to carry out photosynthesis. This, in turn, affects other organisms that depend on these plants for food and oxygen. As a consequence, fish production is reduced. Since light and nutrients are important drivers of phytoplankton and bacterial production, altered abiotic conditions will have important consequences for the aquatic food web base, with implications for the productivity of higher trophic levels (Brett et al., 2017; Lefebure et al., 2013; Liess et al., 2016).As sediments and other suspended solids increase in the water, the amount of light that can pass through the water decreases. Thus, the cloudier the water, the greater the turbidity. There are three major types of particles which are algae, detritus (dead organic material), and silt (inorganic, or mineral, suspended sediment). The major source of turbidity in the open water zone of most lakes is typically phytoplankton. As algae, sediments, or solid wastes increase in the water, so does turbidity. The algae grow in the water and the detritus comes from dead algae, higher plants, zooplankton, bacteria, fungi, etc. produced within the water column, and from watershed vegetation washed in to the water. If light penetration is reduced significantly, macrophyte growth may be decreased which would in turn impact the organisms dependent upon them for food and cover. Reduced photosynthesis can also result in a lower daytime release of oxygen into the water. Effects on phytoplankton growth are complex depending on too many factors to generalize. Very high levels of turbidity for a short period of time may not be significant and may even be less of a problem than a lower level that persists longer. Organic detritus comes from stream or wastewater discharges. Organic matter comes into water from aerial or terrestrial sources (e.g., as falling leaves, in rain, as drainage, etc.) or is generated from within the system (e.g. by photosynthesis and chemosynthesis). Inputs from outside the system are termed allochthonous; autochthonous inputs are generated within the system. The importance of the two types of input will vary with the location of the water body. For example, streams draining through woodlands have large allochthonous inputs, while large lakes and oceans have large autochthonous inputs. In addition to the organic matter contributed by dead bodies, almost all living animals also produce egesta. Ingested food is digested and the remains, together with the waste products of metabolism, are passed out as faeces and urine. The organic composition of faeces varies with the efficiency with which dietary constituents are assimilated and the rate at which faecal matter is produced also varies with food quality. Animals with lower quality diets, like many detritivores, feed almost continuously and produce large amounts of faecal material. In contrast, carnivores have the most nutritious diet and many eat and defecate irregularly as food is often retained within the gut to allow efficient digestion.Sedimentation does not usually spontaneously start increasing in a system; there are reasons for increased. Closer to shore, particulates may also be clays and silts from shoreline erosion, and resuspended bottom sediments. Sediment comes largely from shoreline erosion and from the resuspension of bottom sediments due to wind mixing. On occasion there are natural system changes such as volcanic eruptions or earthquakes that cause debris flows, mud flows, and landslides, or human activities such as clear cuts that cause sudden mass movement. However, most sediment increases are gradual and are caused by changes such as land management, instream alterations, or short-term climatic events. In assessing sedimentation, evaluation of environmental change will help to identify other factors such as precipitation, discharge, shear stress, or a change in channel platform or geometry that may also accompany the sedimentation changes.Dredging operations, channelization, increased flow rates, floods, or even too many bottom-feeding fish such as carp may stir up bottom sediments and increase the cloudiness of the water. High concentrations of particulate matter can modify light penetration, cause shallow lakes and bays to fill in faster, and smother benthic habitats – impacting both organisms and eggs. As particles of silt, clay, and other organic materials settle to the bottom, they can suffocate newly hatched larvae and fill in spaces between rocks which could have been used by aquatic organisms as habitat. Fine particulate material also can clog or damage sensitive gill structures, decrease their resistance to disease, prevent proper egg and larval development, and potentially interfere with particle feeding activities. Dissolved inorganic matter results from solution and weathering processes, either by the water body itself or by indirect inputs like surface drainage and hydrothermal sources. Inorganic particles are common in water which is erosive or which re-suspends sediments. Sand and other mineral grains are swept up by waves on marine and lake shores, and lowland rivers are characteristically turbid as they carry a heavy load of fine inorganic particles. In addition to resulting from erosion, inorganic particles also have biogenic origins. The siliceous frustules of diatoms and the shells of many kinds of invertebrates and protists all result from living organisms, as does coral sand eroded from reefs.Turbidity in lakesThe emphasis in lake studies is different from studies of the stream environment. Because lakes are sediment sinks and essentially closed systems (for sediment), toxins are of great concern. Once a lake has been polluted, it is difficult to clean. Sediment is important in these environments because many inorganic toxins bind to fine sediments. A large percentage of lake sediment literature is aimed towards sediment toxicity. Concern does arise on a regional or national level when mega fauna, such as birds or deer, are affected. This is very different from streams which express environmental changes throughout their systems. Under normal environmental conditions, benthic invertebrates can move quickly enough to keep ahead of fluctuations in natural sedimentation. Artificial dumping and accelerated sedimentation introduces too much sediment too quickly for benthic invertebrate organisms to avoid it (Herdendorf 1992). Case-dwelling mobile macro invertebrate species can do very well in areas of rapid sedimentation because of the decrease in competition and their ability to escape the sediment (Wiederholm 1984). Loss of benthic communities may also occur if an increase in wave action erodes the substrate (Herdendorf 1992). Preferred spawning habitat in lakes can be similar to that in streams, but because of the diverse and relatively more stable environment, spawning occurs in a large variety of substrates. Lake trout in Lake Huron prefer cobble and rubble and do not generally use coarse sands or gravels to spawn. Lake trout, like stream trout, cannot successfully spawn in areas that are covered with fine sediments (Nester and Poe 1987). Other lake species prefer sand, rocks, inshore environments, logs, sticks, plants, or vegetative nests (Herdendorf 1992). Sediment quality in lakes is extremely variable geographically. The introduction of excess fine sediment can be addressed in lake tributaries or in the watershed, but the actual sediment quality is difficult to alter because once it is in the lake, it is hard to remove. Sediment traps such as filter dams and de-silting basins can be used in the tributaries above a lake to reduce the amount of fine sediment that is delivered to the lake (EPA 1973).Dredging of lake bottoms is often considered as a remedial technique to remove excess sediment. Dredging temporarily increases turbidity in the lake and can cause environmental degradation because of the decrease in primary productivity. The sediment may be a nutrient sink and dredging may reintroduce the nutrients back into the lake. The loss of shallow zones may result in the loss of large macrophyte beds, resulting in turn in an increase in the algal population. To further complicate the dredging issue, lakes and other bodies of water are often used for disposal of sludge, which can contain very high levels of toxins. Similar problems exist for river and bay dredging as well. Turbidity in estuariesEstuaries have been studied in depth by numerous disciplines. The use of estuaries by fish is of concern to fisheries management specialists. Most of this knowledge and interest has been limited to the researcher’s own professional peers and has lacked the advantages of interdisciplinary research. The concern for estuaries is growing, and there is a need for practical, useful data and associated management practices. Estuaries have been recognized for their large biomass production and pollution-filtering systems. The emphasis has been primarily on the flora of estuaries and not the fauna, except for bird uses. Estuaries are important for anadromous fish because it is a passage that they must make when migrating from the streams to the ocean or on their return to spawn. Estuaries also serve as a feeding ground and nursery for many fish and shellfish species. Catadromous fish, such as eels, spawn at sea but spend a large portion of their lives in coastal estuaries. Because of the physical, chemical, and biotic diversity of estuarine systems, they are among the most biologically diverse and richest systems found on earth.Estuaries are extremely sensitive to human action. Most large bays have associated large estuaries and also have sizable seaport cities associated with them. A majority of the world’s population lives along the coast line, so estuaries are significantly impacted by land-use practices, recreation, and exploitation. Ship traffic near estuaries can be especially heavy and affects the entire estuarine ecosystem, because it introduces new variables including physical and chemical alterations. Estuaries are also sites of dredging for sand and gravel for industrial and commercial use. A characteristic of estuaries is that their beds are constantly moving because of river inflow and tidal fluctuations. The bedload is composed mainly of sand-sized particles which are easily entrained and move for long distances. The bed material is not always transported in a downstream direction. Depending on tidal influences, material may be moved up and down the channel. Fine silts and clays flocculate in the salt water and are deposited in tidal marshes. The dynamics of sediment transport in and through estuaries is extremely complex. The relative effects of land-use practices or changes were evaluated on the basis of soil erosion and the possible effect that this would have on downstream estuaries. Phillips (1991) found that estuarine sediment is derived from fluvial sediment input, shoreline erosion, and migration of marine sediments inland. Phillips (1991) also indicates that sediment storage is much more environmentally sensitive than basin sediment yield and concludes that dramatic changes in the watershed would be required to alter the sediment budget in the estuary. However, processes that mobilize stored sediment would have a large effect on the sediment budget. Even though sediment delivery may be low, total sediment input can be high. Stopping sediment before it reaches the stream channel is important because once it becomes stored in the channel it can be easily remobilized. Efforts to reduce sedimentation rates will be long-term because large quantities of sediment are already in stream channels due to agricultural and land-use practices. If sediment is in long-term storage in estuaries, rather than en route to the continental shelf, then sedimentation rates should be of great importance. Increased fluvial sediment in estuaries may result in extended tidal marshes, shoaling, infilling of navigation channels, reduction of benthic and aquatic habitat, and reduced primary productivity due to turbulence and limited light penetration (Phillips 1991). Estuaries are utilized by specialized organisms that have adapted to fine sediments, high sedimentation rates, and mobile substrate. The macro invertebrates that are found in the substrate of estuaries are much smaller than those found in streambeds with larger particle sizes. Within the estuary, the density of fauna is commonly greater in the freshwater tidal areas than in other parts of the estuary (Schaffner et al. 1987). The species diversity of macro invertebrates is usually lower in fine-sediment substrates than that in coarser particle substrates. The diversity and evenness of species decline with an increasing percentage of silt/clay and organic matter (Junoy and Vieitez 1990). However, fine-sediment beds are important for burrowing tube-making invertebrates and other.Sediment quality is another widespread problem in freshwater and marine systems (EPA 1992). Sediment quality problems can occur throughout stream types, but tend to occur where there are fine textural stream bottoms and at the lower end of the stream system such as estuaries and deltas. The contaminated sediments can have both direct adverse impacts on bottom fauna, and indirect effects as the toxic substances move up the food chain. Because of the variability of conditions encountered in stream systems, lake systems, estuaries, and oceans, a variety of tests may be needed to characterize the physical, chemical, and biological systems that may be affected. In addition, microbial and benthic species will likely reflect sediment contamination that is not revealed by sampling only fish (Burton 1988). In other words, toxic impacts may be occurring in a river, lake, estuary, or ocean, even though sampling in the water column over the sediments may show water that meets water quality standards. Because there is no single method that captures all the spatial and temporal impacts of contaminated sediment upon all organisms, a compendium has been developed to present several complementary methods to assess sediment contamination (EPA 1992).