TRAVERSE CITY, Mich. — A one-two punch of excessive nutrients and ravenous mussels is causing a sharp drop-off in Great Lakes fish populations and the worst outbreak of algae blooms in decades, says a report released Tuesday.

Runoff from farms, city parking lots and other sources is causing a flood of nutrients such as phosphorus in near-shore areas and bays, the National Wildlife Federation said in a report based on government and university studies. Meanwhile, deeper waters are experiencing the opposite problem: Invasive quagga and zebra mussels are gobbling too much food, causing fish higher up the chain to go hungry.

“This feast-and-famine dichotomy is unprecedented,” said Julie Mida Hinderer, the report’s primary author. “Rapid and drastic ecosystem changes are altering the Great Lakes from top to bottom. The impacts we’re seeing are a sign that the Great Lakes need urgent help.”

A group of scientists warned in 2005 that Great Lakes ecosystems were on the verge of collapse because of a dangerous set of problems, including species invasions and degraded water quality. The wildlife federation report said the scientists’ predictions are coming true.

Toxic algae blooms are on the rise — especially on Lake Erie, the shallowest and warmest of the lakes, where the problem was worse this summer than any time in recorded history, the report said. One gigantic mass of toxic algae, up to 2 feet thick in some spots, stretched across most of Erie’s western basin. The blooms are believed to be causing the return of a “dead zone” in the lake’s central basin with so little oxygen that fish can’t survive.

Other significant algae outbreaks were reported on Lake Huron’s Saginaw Bay and Lake Michigan’s Green Bay. Along Lake Michigan’s coast, extensive blooms of green algae called Cladophora are believed linked to botulism poisoning of fish and shore birds.

Even as algae blooms choke near-shore areas, offshore waters are starved for nutrients because of invasive mussels, which have spread across most of the lakes since their arrival in the ballast water of oceangoing ships in the 1980s. Trillions of quagga mussels, which have mostly displaced the zebra mussels that reached the lakes first, are filtering microscopic plants and animals from the water, leaving too little for competitors that in turn provide food for bigger fish.

On Lake Huron, the biomass or collective weight of deep-water prey fish — which feed popular sport species such as salmon — has dropped 95 percent in the past 15 years. That caused a crash of Huron’s once-thriving salmon fishery, ruining many charter fishing boats, bait shops and other related businesses.

Algae blooms on Lake Erie are forcing charter captains to travel farther in search of prized walleye — a huge expense at a time of thin profit margins and high fuel prices, said Rick Unger, president of the Lake Erie Charter Boat Association. The number of captains licensed in Ohio has dropped from about 1,200 in the 1980s to 700, he told reporters on a conference call.

“I remember what it was like in the ’60s and I don’t want to ever see it like it was then — a fishless, dead lake,” Unger said.

Foreign mussels also have caused a 94 percent decline of tiny freshwater shrimp at the base of the Lake Michigan food chain, endangering whitefish and other native species.

The report calls for stepped-up efforts to reduce near-shore phosphorus overloading — especially programs encouraging farmers to reduce polluted runoff — and tougher policies to prevent species invasions.

Don Scavia, a University of Michigan Great Lakes expert not involved with the report, said it correctly notes the importance of tailoring nutrient control programs to particular watersheds or sections of lakes instead of treating entire lakes the same way. As pollution is generated increasingly by runoff instead of discharges from pipelines, “the one-size-fits-all approach is not appropriate anymore,” he said.