Among the other goals, the initiative seeks an eightfold increase in the amount of urban runoff that its projects capture or treat, and a doubling of wetlands and wildlife habitat that is restored. It would more than double the acreage covered by efforts to control invasive species, from plants to insects to the bighead carp. And it would try to reduce phosphorus fertilizer runoff by more than 1,400 tons by 2019.

The five lakes — the largest group of freshwater lakes in the world — have grown markedly healthier since the 1970s, when a budding environmental movement led to limits on pollution that rescued dying fisheries and made once-fouled shores safe for swimming.

But growing cities have crowded out marshes that hosted wildlife and filtered runoff, and intensive farming has filled rivers with fertilizer that spawns vast algae blooms. The lakes’ ecological balance is also threatened by mussels, lampreys and other invasive species that crowd out or kill native fish and other creatures.

The latest phase will focus on the lakes’ most serious problems, including scores of areas of concern that the United States and Canada identified in 1987 — and that went largely ignored until the restoration initiative began in 2010.

Those 43 areas of concern are largely old industrial rivers and harbors where polluted water and contaminated sediment can pose hazards to wildlife and people.