The opinion of the court was delivered by: Rosemary M. Collyer United States District Judge
The source of this protracted dispute is the Northwest Area Water Supply Project (the "Project" or "NAWS"), a joint venture between the governments of the United States and the State of North Dakota, designed to withdraw water from Lake Sakakawea, a reservoir on the Missouri River, and transfer it across the continental divide in a 45-mile-long pipeline for use in Minot, North Dakota and its surrounding areas. The Province of Manitoba, Canada, sued the Secretary of the Department of the Interior and various officials of the Bureau of Reclamation (collectively, "Reclamation") in 2002, alleging that an April 30, 2001 Environmental Assessment ("EA") and a September 10, 2001 Finding of No Significant Impact ("FONSI") issued in connection with the Project violated the National Environmental Policy Act ("NEPA"), 42 U.S.C. § 4321 et seq. North Dakota intervened as a Defendant. Manitoba argued, inter alia, that Reclamation was arbitrary and capricious under the Administrative Procedure Act ("APA"), 5 U.S.C. § 706(2)(A),*fn1 because it failed to take a "hard look" at the risks and consequences of transferring foreign biota from the Missouri River Basin to the Hudson Bay Basin. The Court ordered Reclamation to complete an EA "that considers an integrated analysis of the possibility of leakage and the potential consequences of the failure to fully treat the Missouri River water at its source" and further ordered Reclamation to "revisit its finding of no significant impact." February 3, 2005 Order [Dkt. # 88] at 1. The Court "permitt[ed] work to proceed [on the pipeline] to the extent it [did] not affect the environment or the NEPA process" but enjoined Reclamation from proceeding with construction that would "influence or alter the agency's ability to choose between water treatment options . . . ." April 15, 2005 Order [Dkt. # 95] at 5 & 6.
On December 5, 2008, Reclamation issued an Environmental Impact Statement ("EIS") addressing water treatment options in the Missouri River Basin. It also reissued the EA and FONSI, which Reclamation incorporated into the EIS. Manitoba, joined by the State of Missouri, who sued Reclamation separately,*fn2 allege that the EIS and incorporated documents violate NEPA. Pending before the Court are all parties' cross motions for summary judgment. Further, Reclamation and North Dakota move to lift the stay; Missouri moves for a permanent injunction. For the reasons explained herein, the Court will deny the motions for summary judgment and the motions to lift the stay filed by Reclamation and North Dakota, grant in part and deny in part the cross motions for summary judgment filed by Manitoba and Missouri, and deny Missouri's motion for a permanent injunction. The Court will order Reclamation to take a "hard look" at (1) the cumulative impacts of water withdrawal on the water levels of Lake Sakakawea and the Missouri River, and (2) the consequences of biota transfer into the Hudson Bay Basin, including Canada.
The Continental Divide separates water flows in the Unites States so that streams flow to opposite parts of the continent. Where it goes through North Dakota, the Divide separates two river basins, the Missouri River Basin and the Hudson Bay Basin. On the southwestern side of the Divide in North Dakota, the Missouri River flows into the Missouri River Basin and eventually drains south to the Gulf of Mexico. On the northeastern side of the Divide, the waters flow north and east into the Hudson Bay Basin.
These Basins have distinct ecological characteristics and contain different species of fish and other aquatic organisms, as well as pathogenic species such as bacteria, viruses, protozoa, fungi, and other microscopic organisms. The co-mingling of untreated water from one Basin into another can result in the introduction of biota - the various life forms of a particular region or habitat - that may be invasive and dangerous to indigenous fish, plants and/or animals. The effect upon fish of "interbasin biota transfer," for example, can be devastating. The introduction of foreign biota can eliminate indigenous species, cause reduced growth and survival rates in indigenous species, and change the trophic structure of fish communities. In documented cases, non-native species have displaced native species through direct competition, predation, inhibition of reproduction, environmental modification, transfer of new parasites and diseases, and destruction of the gene pool through hybridization. See Manitoba, 398 F. Supp. 2d at 45.
For many years, northwestern North Dakota has experienced water supply problems. Many municipalities and small communities in the region, as well as farms and ranches, rely upon groundwater sources that are finite or of poor quality. The largest city in the region, Minot, currently obtains most of its water from the Minot and Sundre aquifers. In the past, these aquifers were recharged by water from the Souris River, which flows south from Canada into North Dakota, takes a wide swing through the northwest part of the state, and flows north back into Canada. However, increased water usage and the construction of two water storage reservoirs in Canada - which reduced flows on the Souris River in the United States - have limited the amount of available water in these aquifers.
The Northwest Area Water Supply Project is a joint federal-state project that "involves the construction of a municipal, rural, and industrial  bulk water distribution system in North Dakota." Compl. ¶ 2. The Bureau of Reclamation, a constituent agency under the Secretary of the Interior, is charged with planning and construction and is accomplishing this in partnership with the State of North Dakota. The primary purpose of the Project is to provide drinking water that meets the "secondary" standards of the Safe Water Drinking Act, 42 U.S.C. § 300f, to local communities and rural water systems in eight to ten counties in North Dakota.
The cornerstone of the Project is the source of the water for NAWS. As presently configured, NAWS would withdraw over three and one-half billion gallons of Missouri River water from Lake Sakakawea every year. The water, which would be partially disinfected and pre-treated south of the Basin Divide, would flow through buried pipelines across the Divide into the Hudson Bay Basin where it would receive final treatment in Minot prior to distribution. The finished water would be delivered by pipeline to communities and rural water systems north of the Basin Divide. Water from the project would drain into the Souris River, which flows into Manitoba.
Reclamation issued a final EA on April 30, 2001, concluding that "[t]he risk of interbasin transfer of non-native biota as a result of the NAWS project is considered low." Compl. ¶ 46. The EA analyzed three alternatives and a no action alternative.
Alternative A included an intake of Missouri River water at either Lake Audubon or Lake Sakakawea, a pre-treatment facility at the intake or at a booster pump station, and upgrade of the water treatment plant ("WTP") in Minot. The pipeline between intake at the lakes and the Minot WTP would be about forty-five miles long and include pumping stations and storage reservoirs. The Missouri River water would be disinfected with ozone or chlorine/chloramine - with a chloramine residual maintained in the pipeline for biofilm control - at a pre-treatment facility on the Missouri River Basin side of the Divide to provide biota transfer control and inactivation of protozoan pathogens and viruses. After reaching the Minot WTP, the pre-treated water would be disinfected further with ultraviolet radiation before being delivered to communities and the rural water systems.
Unlike Alternative A, Alternative B would not have used Missouri River water at all, relying upon the existing water sources in the Hudson Bay Basin. This alternative would have required the drilling of additional wells, some additional pipelines, and other upgrades, but would have eliminated the need for miles of pipeline compared to Alternative A and the Preferred Alternative. It would not have involved the interbasin transfer of Missouri River water.
The Preferred Alternative combined Alternatives A and B and was developed based on the capital costs for both an integrated system and individual treatment systems. Under the Preferred Alternative the Missouri River water would first be partially pre-treated at or near the intake and later treated to "drinking water" standards at the Minot WTP.
Based on the findings in the EA, Reclamation issued a FONSI on September 10, 2001, which stated that a full EIS was not necessary because "[r]easonably foreseeable activities, as described in the EA, will not have adverse ...