The mainstem Missouri River historically carried a large sediment and nutrient load that was important to the evolution and survival of native flora and fauna. These pre-regulation characteristics should be considered in the process of developing water quality standards for the Missouri River.

The federal agencies that are partners in the MRRP, and other major Missouri River ecosystem program and initiatives, should collaborate with ongoing EPA nutrient criteria guidance development process to achieve agreement among themselves and with the states on designated uses for the river, by river segment, to reflect requirements for native species. As a result of this effort, EPA should support states that revise their existing narrative criteria for the mainstem Missouri River in order to reflect requirements for native species, even if such separate narrative sediment and nutrient criteria later are replaced by numeric criteria. As appropriate, downstream considerations (such as Gulf hypoxia) may be considered in the setting of phosphorus criteria.

There has been a good deal of discussion regarding Corps of Engineers habitat restoration actions along the Missouri River that introduce sediment to the main channel. Specifically, some parties have asserted that private entities are held to a higher standard of permitting and monitoring than a federal agency such as the Corps of Engineers. In order to obtain better, more systematic information on sediment dynamics along the river and specific activities that introduce sediment, it is important that all major activities that discharge sediment—whether private sector or governmental—be similarly monitored and evaluated.

All actions by the Corps of Engineers that discharge sediment to the Missouri River either during project construction or through erosion following construction, should be subjected to monitoring requirements for sediment physical and chemical characteristics. This monitoring should be conducted to ensure that sediment or other pollutants discharged to the river comply with applicable water quality criteria.