The Missouri River’s habitat and historic flows have been altered to the point where it is no longer a natural system. Where it was at one time a warm, turbid, wide, braided and slow river; it has now become a cold, clear, dammed, channelized and fast river. Side channels and chutes that allowed species to feed, rest, and reproduce have largely been eliminated. Floodplains have been converted to agricultural and urban lands.

The Corps of Engineers determined in their biological assessment that current management of the river is detrimental to the survival and recovery of the endangered pallid sturgeon and least tern and the threatened piping plover.

Because of this determination, and in compliance with the Endangered Species Act, the U. S. Fish and Wildlife Service and the Corps of Engineers entered into a formal consultation process in April 2000 to address the effects of the operations of the Missouri River on the pallid sturgeon, least tern, and piping plover.

Click here for more information about the Endangered Species Act and Section 7 Consultations

The goal of the consultation was to determine whether current operation of the Missouri River Main Stem Reservoir System, the Bank Stabilization and Navigation Project, and the Kansas River Reservoir System pose jeopardy to the listed species.

Through the consultation process, the Service determined that current operations pose jeopardy to the listed species. The two agencies worked together to develop reasonable and prudent alternatives that will avoid jeopardy.

The biological opinion consists of a description of current river operations, current status of the species, the environmental baseline, and the Service’s conclusion regarding effects of current operations upon the continued existence of the listed species present on the Missouri River.

A biological opinion also includes a list of actions necessary to avoid jeopardizing the listed species.

The biological opinion references hundreds of peer reviewed journal articles; approved reports and documents completed by credentialed scientists at various governmental agencies, universities, and consulting firms; and personal communication with experts. Information was also solicited from basin states, Tribes, and state fish and game agencies.

A biological opinion is generally not reviewed by outside agencies or individuals. However, in this consultation, an independent scientific review group did address questions on habitat and hydrology, particularly as they relate to the river below Gavins Point Dam. The responses to these questions are included unedited as an appendix in the final opinion.

The recommendations of the Missouri River Basin Association overlap many of the recommendations likely to be made in the biological opinion. The MRBA did not address flow modifications below Gavins Point Dam.

Through the consultation, the Service and the Corps developed actions that the Service believes will ensure needed protection for the listed species. These recommendations include the necessary conservation actions contained in the "reasonable and prudent alternative (RPA)" and are designed to return the Missouri to a more natural river system. It is the combination of all parts of the alternative, working in concert, that will eliminate jeopardy to the species. The RPA includes four parts:

1. Flow Enhancement: Implementation of a spring rise and summer drawdown from Gavins Point Dam is necessary to restore spawning cues for fish; maintain and develop sandbar habitat and the associated shallow, slow water habitat needed by birds and fish; and enhance aquatic habitat through connection of the main channel to backwaters and side channels. A spring release from Fort Peck Dam will provide spawning cues and increase the amount of warm water habitat available to pallid sturgeon and native river fish.

2. Habitat Restoration/Creation/Acquisition: A portion of the historic habitat must be restored, enhanced, and conserved in riverine sections that will benefit the listed birds and fish. Habitat restoration goals are 20-30 acres of shallow water (<5 feet deep, <2.5 ft/sec. velocity) per mile. Similarly, variable goals by river segments for emergent interchannel sandbar are also identified.

3. Unbalanced System Regulation: Unbalancing of the upper three reservoirs, when runoff conditions permit, by holding one reservoir low, one at average levels, and one rising on a 3-year rotation will increase the availability of tern and plover habitat in reservoirs in drawdown years; maintain tern and plover sandbar habitat in riverine segments below Fort Peck or Garrison Dams in years of higher releases due to reservoir drawdown; and increase availability of tern and plover sandbar habitat in riverine segments below Fort Peck and Garrison Dams in years of steady or rising reservoir levels.

4. Adaptive Management/Monitoring: Implementation of an adaptive management process that allows efficient modification/implementation of management actions in response to new information and to changing environmental conditions to benefit the species. The two components of this process will be the establishment of an interagency coordination team that will coordinate and guide development and implementation of a robust monitoring program to better understand baseline conditions, analyze actions, and identify modification to improve results.

5. Propagation/Augmentation: The Corps and the Service will work together to increase pallid sturgeon propagation and augmentation efforts, while habitat and hydrology improvements are being implemented. This short-term action will ensure genetic integrity and prevent extinction of existing pallid sturgeon populations. Details of the primary actions of the Reasonable and Prudent Alternative described above and the complementary actions are described in the biological opinion text.

Based on snow pack, the flows will range from 20,000 to 30,000 cfs between mid-May and the end of June. Higher flows would be recommended during higher snow pack years.

The recommendations to modify flows from Fort Peck are aimed at maximizing the amount of warm water habitat available below the dam. The reach of the Missouri River between Fort Peck and Lake Sakakawea is one of the best examples of historic habitat left in the system. Unfortunately, this reach has limited production by warm water species such as pallid sturgeon because of the cold water coming from the dam. Warm water intentionally spilled over the spillway is expected to provide the biological cues to encourage the successful spawning of pallid sturgeon in this reach.

The Service has proposed a spring rise of +17,500 cubic feet per second (total 49,500 cfs) one year out of three and an annual summer low of 21,000 cfs.

These releases will create a semblance of the natural fluctuations of the Missouri River. The rising water in the spring and the lowering of water in the summer will provide biological cues necessary for improved reproduction from species such as least terns, piping plovers and pallid sturgeon.

The rising water washes nutrients into the river. These nutrients are the foundation of the web of life in the river.

The declining water signals the birds that now is the time to nest to ensure the young are hatched with maximum habitat available. Declining water also continually increases water and upland edge habitat that creates feeding zones for shorebirds as they grow throughout the summer. Low flows also create shallow water habitat essential to fish species in the river.

The Service believes modifications below Gavins Point are critical for survival and recovery of the listed species.

Our recommended releases from Gavins Point Dam would not be in effect in the extreme high or low water years. Our recommendations would take effect in the middle 65% of water years. Droughts and floods are important natural events and we would not exacerbate either with our recommendations. Current water conditions will be factored into decision making.

Pallid sturgeon:

Present operation of the Missouri River alters the spawning signals necessary for reproduction. It also limits and fragments remaining habitat and reduces water temperature in specific reaches below dams.

Enhanced spring flows and temperatures from Fort Peck are needed to provide conditions and cues for pallid sturgeon spawning in this reach of the Missouri River.

We expect the flow modifications below Gavins Point to also benefit pallid sturgeon by increasing invertebrate production which drives the food chain for bottom-dwelling fish.

The lower summer flows are expected to benefit pallid sturgeon in the lower 800 miles of the Missouri by providing slower and shallower water to allow young-of-year fish to grow large enough to survive through the first winter. The survival through the larval stage for pallid sturgeon below Gavins Point is thought to be limited due to the excessive steady flows throughout the summer months. Fisheries experts from within the Missouri River basin are virtually unanimous in the opinion that the shortage of slower, shallow water habitat is a major limiting factor for juvenile pallid sturgeon as well as many other species of fish.

Larval and fingerling pallids need to remain in shallow water areas containing high concentrations of food organisms. Under present conditions, the Missouri River is simply too swift and deep throughout much of the lower basin to provide the shallow and slack water habitat where young fish can rest, feed, and grow until they reach a life stage where they are capable of negotiating main channel currents.

These small shorebirds nest on sparsely vegetated sandbars. Higher spring flows scour channels and move gravel downstream creating sandbars that provide resting and nesting habitat for terns and plovers. Higher flows during nest initiation period force birds to nest on the highest sandbars.

Lower summer flows will keep tern and plover nests above water and prevent hatchlings from being washed downstream. It will also allow the birds access to small fish. Open areas with little vegetation also reduces the chances of predation.

We have witnessed on the Missouri River that predation rates are more closely tied to the availability and size of habitat than on whether or not a sandbar is accessible.

Some of the most voracious predators on terns and plovers are other birds, such as owls and crows which are not prevented from reaching tern and plover nests on islands, even in midstream. However, after high spring releases anecdotal research shows that when water levels are lowered in the summer, tern and plover nest predation decreases. This may result from the exposure of much larger areas of sandbars which makes it difficult for predators to find the nests.

Lower summer flows and exposed sand bars will also enhance the reproductive success for least terns and piping plovers because it will allow the birds easy access to small fish needed by adults and chicks.

The unbalanced approach means that the largest three reservoirs - Fort Peck, Lake Sakakawea and Lake Oahe - will all be drawn down approximately one year out of three.

This unbalancing consists of lowering the storage in one lake by approximately 3 feet lower than "normal." The level of the second lake would be held constantly low (drawn down the year before). And the level in the third lake would be raised to inundate at least 3 feet of vegetation that grew around its rim the prior year. This 3-lake cycle would rotate among the upper three lakes on a 3-year cycle.

The inundation of vegetation in the third year provides habitat for spawning fish and for the young-of-year to hide in as they avoid predation by the adult fish and other fish species in the lake. If a larger young-of-year population is raised in a given year, the overall population of the affected species will be larger in subsequent years. By recreating the cycle repeatedly, the long-term prospects will be improved for abundant fish population - whether forage fish or sport fish.

The draw down will benefit the terns and plovers nesting on reservoirs by exposing more shoreline available for nesting.

Adaptive management is an integrated method for addressing uncertainty that focuses on implementing actions, thoroughly monitoring results, and modifying actions when warranted. It can be used to examine alternative strategies for meeting biological goals and objectives. It recognizes that we, as humans, don’t know everything yet regarding the outcome of particular changes.

Adaptive management allows flexibility, responds to various water conditions and species needs, and ensures that future river management will be based on the best available scientific information.

A comprehensive monitoring program is critical to the adaptive management framework. This program will include long-term monitoring which will inventory not only threatened and endangered species, but other fish, birds, aquatic invertebrates, reptiles, amphibians, as well as habitat and water quality. The program will also use focused studies to develop cause-and-effect relationships specific to a given reach or concern. These focused studies will enable scientists to understand and predict the relationship between system operations and the living community of plants and animals.

Piping plovers: This threatened species has been declining for the last 15 years.

Pallid sturgeon: The endangered pallid sturgeon population is in extreme danger of becoming extinct. While spawning may be occurring, there has only been one sighting of a single pallid fry in the last few decades and no evidence yet of surviving one-year-olds. Hatchery stocked fish produced from captured adult spawners have been provided to many of the reaches as an attempt to keep this species from edging closer to extinction.

Least terns: Overall population trends for least terns are positive; however, this positive trend is primarily due to increases in numbers of terns on the lower Mississippi River.