In this Sept. 12, 2013 file photo, a fishing boat cruises on the Milwaukee River near Lake Michigan, an area designated for cleanup because of decades of toxic pollution.

(AP Photo/John Flesher, File)

A new five-year plan to stop toxic pollution, invasive species and farm runoff in the Great Lakes has been unveiled by the Obama administration in hopes that plant and wildlife habitats can be further bolstered.

The plans were released in a new 30-page document called the Great Lakes Restoration Initiative. The study was led by Gina McCarthy, U.S. Environmental Protection Agency Administrator, Wednesday in Chicago at a meeting of mayors from Great Lakes states.

McCarthy said it was a roadmap for federal agencies to"strategically target the biggest threats to the Great Lakes ecosystem."

(MORE: Toxic Algae Blooms Could Become More Common)

Additionally, the plan states that projects starting in 2017 and beyond must factor climate change into their plans. Wetland plants and trees, for example, must be selected for suitability to warmer temperatures, and watershed restorations should be designed to stand up to more frequent and fierce storms.

Congress has appropriated $1.6 billion since 2009 for restoration projects, coordinated by the EPA with support from 10 other federal departments.

The general priorities of the plan "are right on target," said Joel Brammeier, president and CEO of the Alliance for the Great Lakes, adding that he welcomes its new focus on data management and research, and efforts to adapt to climate change.

"Five or 10 years ago, cities were talking about developing climate action plans, but now it seems the smart money has moved beyond that and into building climate resilience," said Brammeier. "It has to be integrated into every part of the work."

Efforts across the eight-state region have included the removal of toxic sediments and invasive plants and the rebuilding of wetlands. The initiative also has supported efforts to prevent Asian carp from reaching the lakes and is targeting runoff from farms and sewage plants that causes noxious algae blooms like those that contaminated the water supply in Toledo, Ohio, this summer.

(MORE: Here's How Toxic Your State's Waterways Are)

The plan calls for increasing voluntary actions by farmers and other agricultural operations, and for slowing runoff in urban areas through projects that include wetland restoration, reforestation and buffer zones between pollution sources and waterways.

Solving the problem of nutrient runoff is possible, but requires "a level playing field that recognizes that pollution is pollution no matter whether it comes from a pipe or from land that is producing our food," Brammeier said.

The administration also will begin evaluating how well projects are meeting their short-term objectives, rather than just long-term goals such as making all fish safe to eat or waters safe for recreation.

Since the initiative began in 2010, five Great Lakes areas that are listed as "areas of concern" because of toxic contamination have been cleaned up, and one area — Presque Isle Bay, in Pennsylvania — has been taken off the list. In the next phase, cleanup should be completed at 10 more sites, according to the plan.

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Algae is seen near the City of Toledo water intake crib in Lake Erie, about 2.5 miles off the shore of Curtice, Ohio.(AP Photo/Haraz N. Ghanbari)