Water Quality (Tech Recommend 10)

Problem Statement

The water quality of the mainstem Snake and Columbia rivers has been significantly altered in the last 150 years. The primary cause of pollution in the Columbia River Watershed is habitat alteration, flow alteration, sedimentation, elevated temperatures, and nutrients. The primary sources affecting beneficial uses of the Columbia River are hydrologic modifications, vegetation removal, stream bank modification, agriculture, and forestry.

In the Columbia River Watershed, the major land uses are agriculture, grazing and forestry. These uses have had considerable impact on the riparian zone through increased stream temperature and stream bank erosion rates, which have serious negative impacts on anadromous fish habitat.

Agriculture, grazing and forestry accelerate erosion and sedimentation providing nonpoint source pollution into the stream system. Sands and coarse silts interfere with the flow of water through spawning gravel and the transport of oxygen to the incubating eggs. High sedimentation rates can also fill deeper pools in streams that are important for overwintering of fish and cold water refuges in the summer.

Sediments can also act as sinks for binding toxic contaminants, reducing their availability to limnetic biota. However, these sinks become sources of toxic contaminantion to the bentic biota. Even when not a significant source, contaminated sediments can provide poorer habitat conditions and indirectly affect anadromous fish habitat.

Removal of stream vegetation causes stream temperature to increase in the summer and decrease in the winter. Elevated summer temperatures have a direct impact on salmon as well as having indirect effects through decreased dissolved oxygen and elevated biological oxygen demand.

The amount of dissolved oxygen in a stream depends on respiration and the biological oxygen demand of substances in the water. Intragravel dissolved oxygen is important to salmon spawning as it provides oxygen to incubating eggs. Agriculture, grazing and forestry have affected intragravel dissolved oxygen by increasing sand and silt to streams.

Nutrients stimulate algal growth, which increases the biological oxygen demand and thereby decreases minimum dissolved oxygen. Many of the waters of the Columbia River Watershed have problems with excess nutrients. Nutrients come from a number of sources including animal wastes, fertilizers, sewage treatment plants and some industrial effluents.

In addition, toxic pollutants have been introduced to the rivers from numerous man-made sources. Federal, municipal, and industrial facilities are the major sources of hazardous chemicals and radionuclides. Industrial pollutants, such as fluoride, have been demonstrated to delay adult salmon migration (Damkaer and Dey 1986). Pesticides and other persistent highly toxic chemicals in fish tissue and sediment are present in samples collected from the Columbia River Basin. In the lower 150 miles of the mainstem Columbia River, where all migrating Columbia River salmon must pass, the states of Oregon and Washington have found that the following toxic pollutants are above guidance levels for fish tissue and sediments: Organo-chlorines (DDT, DDD, DDE, PCB, aldrin, dieldrin, endrin, trichlorobenzene, and PAHs), mercury, cyanide, arsenic, chromium, iron, nickel, pyrene, silver, zinc, cadmium, and copper (Tetra Tech 1993). These and other contaminants are known to adversely affect salmonid species.

Quantitative data characterizing the interaction of water quantity and water quality in the Columbia River Watershed is scarce, however, water quality and flow modification have the most likely impact on fisheries. Less quantity means less dilution and therefore higher concentrations of pollutants. Any stresses imposed on young fish by changes in river flows or water levels will be exacerbated by the presence of contaminants such as pesticides from agriculture, sedimentation from agriculture, grazing, logging, development, or mining; heavy metals from ore processing and other industries; and sewage effluent. Other stresses arise from deposition or removal of sediments resulting from changes in river flow; the accumulation of hazardous substances in slackwater versus free-flowing; the eutrophication processes of slackwater; and the influence of changes in the lower estuary where salmonid smolts physiologically adjust from freshwater to the marine environment.

The following water quality concerns have been identified by the U.S EPA for the Columbia Mainstem:

  • Columbia River estuary: Temperature, PCBs, dioxins, furans, pesticides, metals, and bacteria.
  • Mainstem below Bonneville Dam: Temperature, PCBs, dioxins, furans, pesticides, metals, bacteria, dissolved oxygen (DO), and total suspended solids.
  • Mainstem, Bonneville Dam to Priest Rapids: Total dissolved gases, temperature, dioxins, furans, pesticides, PCBs, and metals.
  • Mainstem Snake, mouth to Hells Canyon: Temperature, sedimentation, total dissolved gases, algae, nutrients, DO, and organics.
  • Snake Mainstem above Hells Canyon Dam: Temperature, sedimentation, pH, bacteria, ammonia, algae, nutrients, DO, and pesticides.
  • Mainstem, Priest Rapids to Chief Joseph: Total dissolved gases, dioxins, furans, pesticides, metals, and temperature.
  • Mainstem Chief Joseph to the Canadian Border: Metals, dioxin, furans (Lake Roosevelt), and bacteria.


The implementation of comprehensive protection and restoration actions will greatly reduce nonpoint and point source inputs into the Columbia River Watershed. These actions must be taken at the federal, state, local, and tribal level.

A comprehensive review and monitoring program for water quality parameters known to affect salmon, lamprey, sturgeon, and the food sources upon which they depend in the mainstem Snake and Columbia rivers is needed to target pollution abatement programs to benefit salmon survival and protect human health.

Reducing and eliminating known sources of persistent, bioaccumulative toxic chemicals and heavy metals will assist in reducing salmon exposure to these pollutants and the risk of salmon abnormalities and mortalities associated with such exposure. Abnormalities may include bodily and glandular tumors and lesions and endocrine imbalances affecting salmon reproduction and cellular development. Mortalities may be from diseases, such as bacterial kidney disease, and from bioaccumulation of toxic pollutants.

Recommended Action/Test

  • Immediately undertake adaptive management activities, through restoration and protection actions, to reduce or eliminate nonpoint source impacts. These actions are identified through the subbasin plans in Volume II of this document.
  • Implement a comprehensive review and monitoring program for water quality and substrate parameters affecting salmon, lamprey, and sturgeon and their food sources.
  • Implement a biomonitoring program that: 1) identifies levels of organochlorine compounds, heavy metals, and radionuclide isotopes at various points in the mainstem Columbia and in salmonid species and sediments; 2) documents physiological abnormalities, especially in fish reproductive organs; 3) identifies hormone protein levels in fish blood samples as an indicator of the presence of organochlorine compounds; and 4) identifies sources of contaminants.
  • Prohibit all known permitted sources of persistent, bioaccumulative toxins affecting anadromous species or their habitat in the Columbia River Basin.
  • Reduce discharges of other contaminants to meet water quality criteria fully protective of designated beneficial uses for anadromous fish.

Expected Results

A comprehensive review and monitoring program will identify pollutant sources and assist in compliance efforts. Eliminating known, permitted sources of heavy metals and persistent, bioaccumulative toxins will reduce physiological abnormalities and hormone and sex-specific protein imbalances in Columbia River salmon. Results from the proposed bio-monitoring program will indicate the scope and degree of salmonid exposure to toxic pollutants and heavy metals and may prompt new priorities in mainstem habitat protection and remediation.

Institutional/Decision Structure

Tribal, federal, state, and local governments should implement actions to reduce the input of point source and nonpoint source pollutants in the Columbia River Watershed. Restoration actions implemented through Volume II of this document will reduce nonpoint source pollution.

Tribal governments and state and federal agencies, in coordination with CRITFC, will coordinate a water quality parameter review and biomonitoring program. Tribal staff and CRITFC will coordinate field collections of fish tissue and blood samples. An independent laboratory will be selected to perform tissue and blood analyses. These activities will be funded by the U.S. Environmental Protection Agency.

State water quality agencies and the Environmental Protection Agency will need to modify pollu-tant discharge permits to assure elimination and reduction of pollutants.


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