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Linking Restoration Practices to Water Quality Parameters

Because water resource quality is defined by all its components—the chemical, physical, and biological— adequate understanding of the relationships among physical, chemical, and biological processes is critical for determining when restoration can be used to improve stream quality. This chapter illustrates the relationship between several restoration techniques and a number of water quality parameters. Discussion in this chapter is based on two key concepts:

  • Ecological restoration techniques can be effective in meeting water quality standards, including numeric and narrative criteria and designated uses, and
  • Ecological restoration techniques can be evaluated and implemented within the framework of the TMDL process.

Chapter 3 describes how certain ecological restoration techniques affect numerous water quality parameters, thus illustrating how restoration can be used to address non-compliance with designated uses and numeric and narrative water quality criteria. Relative effects of selected stream habitat restoration techniques on several water quality parameters are summarized in Table 3-1

Altered Stream Geomorphology

Geomorphological characteristics such as pool-riffle ratios, width/meander length ratios, width/depth ratios, and substrate composition may impact stream ecology. Long-term trends in stream geomorphology may also exacerbate impairment caused by other sources. A stream can be characterized and classified based on its geomorphology, e.g., form and pattern, and channel behavior. In addition, classification "also can indicate how restoration might be approached if a reach of river becomes aberrant or different from its normal conditions" (Leopold 1994). For instance, in a stream where land-use changes have resulted in downcutting of the channel, increased suspended sediment loads may occur, as well as destruction of fish and wildlife habitat by erosion. In some cases, upland restoration techniques in the surrounding watershed (such as restoration of natural hydrologic regime and the re-establishment of wooded riparian buffers) may sufficiently allow a system's geomorphology to restore itself. Restoration techniques based on interpretation and control of stream geomorphology generally must take into account dynamics of flow and sediment transport throughout an entire watershed.

It is important to note that the restoration techniques listed below for altered stream geomorphology and the other parameters discussed in Chapter 3 cannot be developed or applied in isolation. As described in Chapter 4, a mosaic of restoration techniques must comprise a watershed approach mitigation plan. The following techniques could be considered for altered stream morphology:

  • Reworking the stream channel to restore structural complexity (e.g., thalwag) and natural flow patterns (e.g., sinuosity and meander). For some of the most severely degraded channels, heavy equipment may be necessary to reconstruct the channel.
  • Strategically insert structures (e.g., log and gabion drop structures, large boulders) into the channel.
  • Mitigate upland land use practices that result in damaging hydrological regimes.
  • Evaluate operation of dams and other flow diversion structures to more closely simulate natural flow conditions.

Fine Sediment Loads

Excessive loads of fine sediments are detrimental to most stream systems because they can alter both substrate and water column conditions. Alterations in substrate conditions may contribute to a decline in fish spawning success, particularly salmonids. Fine sediment can trap fry that are attempting to emerge; deplete intergravel oxygen levels, smothering eggs that have been laid; limit the aquatic invertebrate populations used as a food source by predatory fish in rearing areas; and fill the pools and pockets between rocks and boulders on which young fish depend to protect themselves. Suspended fine sediments may also influence the survival of aquatic organisms by clogging and damaging respiratory organs. Increased turbidity increases water temperature (because turbid water absorbs heat more efficiently) and suppresses algal photosynthesis. Some aquatic ecosystems, however, where suspended solid concentrations were naturally high, such as the lower Colorado River system, have been adversely impacted by dams that reduced natural sediment transport.

For many streams, reduction in natural sediment loads can adversely affect channel stability and ecological conditions. When flowing waters have very low sediment concentrations or are devoid of sediments, they scour sediments from the stream banks and beds until an equilibrium load is suspended in the water. This scouring can degrade the morphology of the affected channel. Also, fine sediment is a natural, if not essential, part of most aquatic systems, except when present in excess. Beschta and Platts (1986), for example, note that the optimal spawning substrate appears to consist of gravel with a small amount of fine sediment and rubble to support egg pockets and stabilize the beds during high flows. Reservoir construction, in particular, can cause unnaturally low downstream sediment loads and high flow energies. Both factors produce channel degradation downstream, characterized by increased stream depth and increased channel straightening; in contrast, upstream channels are affected by sediment aggradation, characterized by decreased stream depth and increased meander patterns. Erosion is always greater downstream of reservoirs than in natural streams having otherwise similar characteristics. Typically, this erosion begins in the stream reaches nearest the dam and continues until limited by natural factors within the channel (e.g., the accumulation of materials resistant to erosion, including large particulates and/or cohesive silts and clays that clog the streambed). Strongly established riparian plant communities also can be important deterrents of bank degradation.

Restoration techniques that can restore equilibrium to sediment loads to streams include:

  • Changes in land-use practices that reduce sediment loading, such as conservation tillage, contour farming, sodding or wildflower cover during construction activities;
  • Restoring wetlands to intercept sediments;
  • For some systems, manipulating discharge depths from the reservoir to increase fine sediment discharges;
  • Augmenting reservoir discharges with "silt runs" of added fine sediment (very limited application); and
  • Removing the reservoir (a rarely used management option). Natural tributary inflows to regulated streams downstream of reservoirs can contribute the necessary suspended materials to help the stream to achieve an equilibrium sediment load, hence reducing the erosive nature reservoir discharges.

Upland techniques may be applied in combination with instream techniques to mitigate instream sediment impacts, such as degraded substrate condition. Instream restoration, however, is unlikely to succeed unless sources and causes of excess suspended solid loading are addressed simultaneously.

Abnormally High Stream Flows

High-energy flows can erode substrate and bank materials, destabilize the physical structure of aquatic habitats, kill resident aquatic organisms, and destroy eggs incubating in the benthic environment. Seasonal cycles of high-energy flow events (e.g., spring floods) are typical in most aquatic systems; habitat alteration and degradation, however, may exacerbate impacts of high-energy flows and contribute to impairment of designated uses. For instance, in a channelized stream with minimal riparian vegetation, flow velocity and volume will likely be much greater than would be expected in a "natural stream", thereby increasing its erosive potential.

Instream and riparian techniques that can mitigate such impacts include

  • Restoring natural stream meander and channel complexity;
  • Increasing substrate roughness;
  • Promoting growth of riparian vegetation, which serves as a drag on flows;
  • Land use modification along buffers and other source areas; and
  • Plunge pools and flow baffles to decrease the high energy of discharged waters.

These instream practices may need to be accompanied by techniques applied in the surrounding watershed, such as upland revegetation or the establishment of nonpoint source BMPs.

Low Flows

Maintaining flow is often essential to habitat protection. In many regions of the United States, stream segments are periodically dewatered from irrigation, industrial, and municipal withdrawals; diversion for hydroelectric power; evaporation; and groundwater infiltration. Additionally, during low-flow conditions, impacts from point source discharges of chemical stressors are typically greatest, because effluent constitutes a larger percentage of (sometimes all) stream water at low flow, with increased pollutant concentration. NPDES permits based on low flow conditions (e.g., 7Q10) often cannot anticipate various combinations of climatic conditions and water demand that lead to exceedingly low flows.

Impacts attributable to minimum flows can be mitigated by several instream restoration techniques, including

  • Reducing channelization,
  • Restoring wetlands to store water and thereby restore natural hydrologic regimes,
  • Controlling evaporation through restoration of the riparian canopy,
  • Replacing exotic riparian plant species that have high evapotranspiration rates with native species that have lower transpiration rates,
  • Constructing drop structures to create pools that provide protection for aquatic life during low-flow periods,
  • Increasing channel depth and undercut banks to provide areas for protection of fish and other species during periods of low flow, and
  • Increasing groundwater recharge to streams through increased infiltration (e.g., reduced imperviousness in recharge areas).

Minimum flows can also be addressed by applying techniques in the surrounding watershed, such as managing watershed land use to prevent excessive dewatering.

Resource management agencies, for example, can encourage or allow beavers to colonize stream segments; beaver dams create wetlands and retain water that supplements low flow during dry periods. Restored wetlands can have the same effect as a beaver dam. Local zoning authorities have begun to encourage the reduction of impervious area in watersheds through land-use ordinances. Increased infiltration and reduced peak flows from rapid runoff contributes to a more sustained base flow to the stream from groundwater discharge.

Restoration practices to mitigate low velocity/low-flow conditions often require close collaboration with other resource management agencies (e.g., USDA Forest Service), zoning authorities (e.g., county governments), and agricultural extension agencies. Several agricultural activities contribute to low velocity/low flow conditions. Agricultural extension agencies have developed specific techniques to modify the practices that impact streams and rivers in this manner. For example, irrigation plans can be optimized to reduce the demand for water that is diverted directly from the stream or dewatering by overdrafting an adjacent aquifer. Changing crop rotations and using less water-intensive crop alternatives are other tools that have been used effectively to address low velocity/low-flow situations.

Biological Integrity

Practices that improve chemical and physical habitat quality will positively affect biological integrity, because improvements in water and habitat quality generally increase biodiversity and improve ecological functions such as nutrient and energy cycling, trophic relationships, and predator-prey relationships.


As discussed in the previous section, all of the restoration practices described in Table 3-1 potentially reduce ammonia toxicity. These same practices would, through similar mechanisms, reduce the toxicity of other substances (e.g., hydrogen sulfide). Wetlands can also help reduce the toxicity of some metals, by reducing metal concentrations and metal bioavailability. Together, all these practices would help reduce the total toxicity of the water and help attain this narrative water quality standard.

Algal Growth

Streams having slow flow waters, warm temperatures, and highly elevated nutrient concentrations can develop nuisance growth of algae (in general, concentrations of total inorganic nitrogen greater than about 0.25 mg/l and dissolved phosphate of about 0.02 mg/l are viewed as potentially leading to nuisance algal growth). Beyond the appearance, odor, and taste problems normally associated with nuisance algal growth, various instream problems can also result. For example, dense growths of filamentous algae in streams can block access to microhabitat features important for the growth and survival of many small or young aquatic species. Further, few aquatic species can use filamentous algae for food. The rapid and abundant growth of filamentous algae tend to competitively reduce the abundance of other algal forms that potentially provide favorable food sources for various aquatic species. Thus, nuisance algal growth tend to reduce available food supplies and, therefore, growth potential for many aquatic species.

Most importantly, both the high metabolic demands by the dense algal growths and the decay of the many dead algal filaments can drive down oxygen concentrations (especially at night-time) in the affected surface water. Often these demands can lead to depletion of dissolved oxygen concentrations. In turn, this can lead to severe stress or death of many species, loss of aquatic populations, and substantial shifts and simplification of aquatic communities. Generally, these changes also reduce the potential remaining assimilative capacities of receiving waters for other pollutants and reduce the resistance of the remaining stream community to other potential pollutant stressors. Additional concerns related to low dissolved oxygen concentrations are discussed in the next subsection.

In many streams, conditions promoting nuisance growth of algae can lead to stimulated growths of higher aquatic plants (macrophytes). Excessive growths of macrophytes can lead to many of the same problems caused by nuisance algal growths. In addition, dense macrophyte growths also can lead to additional slowing of flows and warming of waters, in some cases further intensifying the magnitude of these problems.

The following instream, riparian, and upland restoration practices can help to reduce excessive growth of algae and macrophyte.

  • Drop structures and riffles would create turbulence that would reduce attached algal growth;
  • During some periods of the year, wetlands will reduce nutrient input into the stream, thereby reducing algal growths;
  • Planting trees and bushes will reduce the amount of sunlight available for algal growth, thus leading to reductions in algal growth;
  • Increased channel depth and undercut banks will reduce the area available for algal growth; and
  • Nonpoint control of nutrient loading.

Low Dissolved Oxygen Concentrations

Low dissolved oxygen (DO) concentrations can be detrimental to aquatic life. DO concentrations in surface waters are determined by many factors, including water temperature, salinity, biological respiration, chemical oxygen demand, sediment oxygen demand, photosynthesis, and transfer of oxygen into the water from the atmosphere (i.e., re-aeration). While DO concentrations are known to fluctuate throughout the day, minimum DO concentrations in streams typically occur at night when aquatic plants do not photosynthesize but aquatic organisms, including plants, respire. The lowest daily DO concentrations generally occur immediately before dawn.

In most streams that do not receive significant input of materials with high chemical and biological oxygen demand and nutrients that stimulate plant growth and respiration, natural re-aeration will maintain adequate DO concentrations to support a healthy aquatic community. Natural re-aeration rates in a stream are influenced by stream properties such as depth, turbulence, frequency of riffle areas, and natural drops (e.g., waterfalls and natural obstructions that create turbulence). Disturbances such as channelization and excessive erosion reduce channel complexity and thus re-aeration potential. Types of restoration practices that can increase DO concentrations include the following:

  • Reintroducing or constructing small hydrologic drop structure or other structures (e.g., boulders, logs) that increase hydrological turbulence and mixing that increase re-aeration rates;
  • Restoring existing degraded wetlands or re-establishing natural streamside vegetation to intercept nonpoint sources of nutrients to reduce aquatic plant growth and respiration demand within the stream;
  • Re-establishing trees and bushes along stream banks to reduce incident sunlight and water temperature, and to trap nutrients and sediments, thereby reducing aquatic plant growth and respiration demands;
  • Restoring stream depth and undercut banks and re-narrowing stream width to reduce aquatic plant growth and water temperatures, thereby reducing respiration demands; and
  • Re-establishing or creating, shallow riffle substrates to increase turbulence, mixing, and the area of stream surface exposed to the atmosphere, which will increase re-aeration rates.

Altered Temperature

Abnormally high water temperatures may adversely impact aquatic life. Increased water temperature also increases toxicity of many chemicals such as un-ionized ammonia. High water temperatures reduce DO concentrations by increasing plant growth and respiration rates and decreasing the solubility of oxygen in water. Solar heating is the primary cause of abnormally high water temperatures. In some streams (e.g., warm water rivers downstream of dams with hypolimnetic discharges), abnormally low water temperatures may adversely affect warmwater aquatic life. Types of instream, riparian, and upland habitat restoration practices that can be used to manage water temperatures include:

  • Re-establishing trees and bushes along stream banks to reduce incident sunlight;
  • Restoring stream depth, re-establishing undercut banks, and narrowing stream width to reduce excessive solar warming; and
  • Retrofit dams with multilevel intake to control temperatures.

Extreme pH

Rapid fluctuations or sustained changes in pH outside the pH range that an organism has become accustomed to can create conditions that are stressful, or even toxic. In particular, aquatic organisms may suffer an osmotic imbalance under sustained exposures to low pH waters.

The concentration of hydrogen ions in aqueous solution is expressed as pH. The pH scale is a relative measure of the acidity of a solution, ranging from very acidic (pH of 1) to very alkaline (pH of 14). Neutrality occurs at a pH of 7. Most natural waters are circumneutral (i.e., near pH of 7), with pH values ranging from 6 to 8 (Stumm and Morgan 1981).

The carbonate buffering system controls the acidity of most streams. Carbonate buffering is an equilibrium between calcium, carbonate, bicarbonate, carbon dioxide, and hydrogen ions in the water and carbon dioxide in the atmosphere. The amount of buffering, also called alkalinity, is primarily determined by carbonate and bicarbonate concentration, which are introduced into the water from dissolved calcium carbonate (i.e., limestone) and similar minerals present in the watershed. In general, higher alkalinity makes water more resistant to acidification.

Acidification occurs when all alkalinity in the water is consumed by acids, a process often attributable to the input of strong mineral acids (e.g., sulfuric acid) from acid mine drainage and acidic precipitation or weak organic acids (e.g., humic and fulvic acids), which are naturally produced in large quantities in some types of soils, such as those associated with coniferous forests, bogs, and wetlands. In watersheds with relatively large amounts of limestone (or similar alkaline, rapidly weathered minerals), surface waters are well buffered and therefore resistant to acidification. Waters most susceptible to acidification are found in watersheds with minerals that weather slowly (e.g., granite) and have little or no limestone or other alkaline minerals.

Another characteristic of pH in some poorly buffered surface waters is high daily variability in pH levels attributable to biological processes that affect the carbonate buffering system. Extreme increases in pH may create conditions as detrimental to aquatic organisms as low-pH conditions and contribute to the buildup of toxic concentrations of un-ionized ammonia (NH3), a toxic form of nitrogen. In waters with large standing crops of aquatic plants, uptake of carbon dioxide by plants during photosynthesis removes carbonic acid from the water, which can increase pH by several units. Conversely, pH levels may fall by several units during the night when photosynthesis does not occur and plants respire carbon dioxide, which is converted to carbonic acid in the water. The following instream, riparian, and upland restoration practices can be used to reduce acidity or stabilize extreme fluctuations in pH levels:

  • pH levels can be increased by restoring existing degraded wetlands that intercept acid inputs such as acid mine drainage and help neutralize acidity by converting sulfates associated with sulfuric acid to insoluble non-acidic metal sulfides that rema in trapped in wetland sediments.
  • Techniques discussed above for increasing DO concentrations also tend to stabilize highly variable pH levels attributable to high rates of photosynthesis.

Ammonia Toxicity

Ammonia can be toxic to aquatic life and has been found to be a source of toxic effects to aquatic life in some streams. Ammonia, an inorganic form of nitrogen, is a product of the metabolism of organic nitrogen and the biological conversion by bacteria of nitrate to ammonia in anaerobic waters and sediments. Inadequately treated municipal wastewater, agricultural runoff, groundwater contamination by fertilizer, stormwaters, and feedlots are potential sources of ammonia and nitrate to streams.

The un-ionized form of ammonia exists in equilibrium with the ammonia and hydroxide ions. The reaction occurs rapidly and is controlled by pH and temperature. Monitoring and water quality models usually report total ammonia, and the un-ionized fraction must be estimated. As weight per volume of N, un-ionized ammonia concentrations are determined from total ammonia (NH3+NH4+) as (Bowse et al. 1985):

Pkn = 0.09018 + (2729.92/(T+273.2))
where A is the measured total ammonia concentration and pKn is the hydrolysis constant, which depends on temperature:
NH[subscript 3] - N[subscript 9]mg/1 = (14,000 * A)/(1+{10[superscript pk[subscript n] -pH]})
where T is temperature in degrees Celsius.

Ammonia is present in water in two forms, un-ionized (NH3) and ionized (NH4+) ammonia. Of these two forms of ammonia, NH3 has relatively high toxicity and NH4+ has relatively negligible toxicity. The proportion of NH3 is determined by the pH and temperature of the water: As pH or temperature increase, the proportion of un-ionized ammonia and the toxicity increases. For example, at pH 7 and 68 oF, only about 0.4% of the total ammonia is in the form of NH3, while at pH 8.5 and 78 oF, 15% of the total ammonia is in the form of NH3. Consequently, ammonia is over 35 times more toxic at pH 8.5 and 78 oF than at pH 7 and 68 oF.

Any instream, riparian, or upland restoration practice that decreases pH or temperature will decrease the potential toxicity of ammonia to aquatic life in streams:

  • Restoring or enhancing the re-aeration potential of the stream can reduce ammonia concentrations by providing more DO for biological oxidation of ammonia to nitrate and by increasing the volatilization of ammonia into the atmosphere. The re-aeration potential can be increased by constructing small drop structures, riffles, and other structures that increase turbulence and mixing.
  • Restoring wetlands that will intercept nutrients, thus reducing plant growth and photosynthesis in the stream, thereby decreasing pH levels, and also reducing ammonia concentrations, both of which will reduce ammonia toxicity.
  • Re-establishing trees and bushes along stream banks to reduce incident sunlight and water temperature and trap nutrients, thereby reducing aquatic plant growth and photosynthesis; and
  • Restoring stream depth and re-establishing undercut banks and narrowing stream width to reduce aquatic plant growth and decrease water temperatures.
  • Reducing nonpoint source inputs of nutrients (e.g., nitrogen, phosphorus) to streams.

The decline of pH in response to these restoration measures is adequate to mitigate the accumulation of high concentrations of ammonia. However, the pH shift is generally not large enough to present a problem for increased mobilization of metals (e.g., aluminum, selenium, arsenic, mercury) from sediments. Generally, these metals are mobilized at a pH much lower than those associated with ammonia toxicity.

Toxic Concentrations of Bioavailable Metals

The uptake of metals by aquatic life is an active, rather than a passive, biological process. Because the primary pathway for most metal uptake by aquatic life is through respiratory organs of fish and aquatic invertebrates, and only ionic forms of metals can pass through cell membranes, the toxicity of most metals to aquatic life is a function of the concentration of dissolved ionic forms of metals in the stream. Consequently, particulate metals are not directly toxic to most forms of aquatic life.

Many toxic substances, including metals, have a tendency to leave the dissolved phase and attach to suspended particulate matter. The fractions of total metal concentration present in the particulate and dissolved phases depend on the partitioning behavior of the metal ion and the concentration of suspended particulate matter. The dissolved fraction may also be affected by complexing of metals with organic binding agents.

The primary mechanism for water column toxicity of most metals is adsorption at the gill surface. While some studies indicate that particulate metals may contribute to toxicity, perhaps because of factors such as desorption at the gill surface, the dissolved metal concentration more closely approximates the fraction of metal in the water column which is bioavailable. (1) Accordingly, the EPA's policy is that the use of dissolved metals to set and measure compliance with water quality standards is the recommended approach (EPA 1993c).

Conditions that partition metals into particulate forms (presence of suspended sediments, dissolved and particulate organic carbon, carbonates, bicarbonates, and other ions that complex metals) reduce potential bioavailability of metals. Also, calcium reduces metal uptake, apparently by competing with metals for active uptake sites on gill membranes. pH is also an important water quality factor in metal bio-availability. Metal solubilities, and therefore the proportion of ionic forms of most metals, are lower at circumneutral pH than in acidic or highly alkaline waters. In general, as concentrations of all these water quality factors increase, the proportion of less toxic particulate metal increases. Therefore, any restoration technique that increases the concentration of these water quality factors potentially reduces metal toxicities.

A number of instream, riparian, or upland restoration techniques can decrease the toxicity of metals to aquatic life by either reducing input of metals to streams or by altering appropriate chemical parameters in order to increase the proportion of less toxic particulate metals:

  • Techniques mentioned above for stabilizing pH. These techniques decrease metal bioavailability by increasing particulate metals.
  • Restoring existing wetlands to treat acid mine drainage is a good example of such a restoration practice. Wetlands can reduce metal inputs and increase inputs of dissolved organic carbon and alkalinity concentrations to streams, all of which reduce metal toxicities.
  • Re-establishing trees in riparian areas and encouraging the growth of other riparian vegetation can also help reduce concentrations of bioavailable metals by trapping within or filtering metals from nonpoint sources and by contributing particulate and dissolved organic matter to the stream.


  1. Certain metals, most notably mercury, also cause toxicity through other routes of exposure. Under anaerobic conditions, methanogenic bacteria in the sediment can produce methyl mercury, which is soluble and highly toxic and can accumulate through the food chain.  Return to text

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