Managing fish populations in Minnesota’s iconic walleye lakes gets trickier with each passing year.

The earth is warming, invasive species are proliferating and fishing pressure in the electronic age is ever more intense. Gone are the days when fisheries managers could stay ahead of the curve by annually measuring the abundance or scarcity of a target species or key forage fish.

A new study by the Department of Natural Resources (DNR) is digging deeper. Funded by tax money allocated last month by the Minnesota Aquatic Invasive Species Research Center, researchers are prying into what’s going on in the food chains below and around walleyes in nine of the state’s 10 largest walleye lakes.

They’re looking for answers on how to sustain the official state fish in the face of lake-altering nutrient consumption by trillions of hungry zebra mussels and spiny waterfleas.

“By the time adult walleye populations are showing a trend, other stuff has been changing for quite some time,’’ said Gretchen Hansen, the DNR fisheries ecologist who is leading the study.

By examining walleye diets and the diets of small and large living things all around them, resource managers can track changes in the distribution and availability of forage and watch how walleyes cope. Ideally, the information will help the DNR detect stress earlier and respond faster with fishing regulations to sustain walleye populations before they crash.

Hansen said the two-year, $200,000 study will look separately at the food webs in Mille Lacs, Leech, Upper Red, Rainy, Cass, Winnibigoshish, Vermilion, Kabetogama and Lake of the Woods. Red Lake is the only one in the group not infested by zebra mussels or spiny waterfleas. Mille Lacs is the only one infested by both invaders. The rest are contaminated by one or the other, and each lake receives unique management attention for walleyes.

Together with zebra mussel-infested Lake Pepin, which is not included in the study, the big lakes account for 40 percent of the annual statewide walleye harvest and make a significant contribution to the $2.4 billion spent each year on fishing in Minnesota.

Nick Phelps, director of the invasive species research center, said Hansen’s study fits a high-priority need to bolster DNR fisheries management. If zebra mussels and spiny waterfleas can’t be eradicated, he said, the state must learn to manage walleyes in the face of those enemies. Zebra mussels have proven to be the most troublesome, spreading in Minnesota at a rate of 20 to 30 water bodies each year despite expenditures of more than $10 million a year to stop them.

Phelps said the Natural Resources Research Institute at the University of Minnesota Duluth is collaborating in the study, which likely will roll into subsequent phases beyond 2019.

Scientists already know that zebra mussels and spiny waterfleas bully native fish by hogging microscopic and near-microscopic plankton of the plant and animal varieties. Levels of zooplankton — the animal variety — have declined and remain suppressed in the aftermath of species invasions in Mille Lacs, Rainy, Kabetogama, Lake of the Woods and Vermilion, according to the DNR.

In recent weeks, Hansen’s study crews netted baby fish, minnows and invertebrates from Upper Red Lake, Leech and Mille Lacs. Those species, which walleyes rely on for food, link closely to zooplankton and are thought to be most immediately affected by any decline.

“We’re looking to understand the food webs supporting walleye and how zebra mussels and waterfleas disrupt the web,’’ Hansen said. “When that happens, how does it play out?”

As part of the study, baby walleyes captured in the nettings will be analyzed for growth rates compared to historical data. Said Hansen: “If fish in the first year of life are affected [slow to grow], how is that transmitted up to adult populations?’’

The answers could be different in each lake because organisms at all levels of the food chain can adapt differently to change. The goal is to develop baseline data and then track developing imbalances in who is eating who. The method is not to examine the stomachs of various creatures. Rather, the researchers will gather tissue samples for molecular analysis to paint a picture of what they’ve been eating over the course of months. Tissue samples from adult walleyes, bass, northerns and other fish will be collected during traditional population surveys achieved with fall nettings.

Hansen said her team will be quick to collect samples from Red Lake and Leech, in particular, because neither water body is infected by adult zebra mussels. It’s an opportunity to gather a snapshot of food web interactions when the lakes are healthy.

The DNR last fall designated Leech Lake as infested by zebra mussels when larval stage colonies were detected in two locations. Those hatches have yet to explode in the expansive lake in Walker, Minn., but when they do the beloved walleye fishing destination will be saturated with adult zebra mussels in three to five years.

Hansen said walleyes are traditionally managed for how they are connected to perch, tullibee or other forage fish. But in the absence of high-tech tissue analysis, managers don’t know the depth of those connections or how walleyes adapt when an important forage base shrinks.

The type of data now being collected in Hansen’s study is what fisheries biologists have longed for in understanding the steep walleye decline in Mille Lacs that began around 2000 and accelerated around 2010 with the advent of zebra mussels and spiny waterfleas.

Paul Venturelli, a former University of Minnesota fisheries biologist who headed the 2014 “Blue Ribbon Panel Report’’ on Mille Lacs walleyes, said the scientists who reviewed the crisis were left to speculate on causes of the decline. For instance, if Mille Lacs walleyes once preyed heavily on lake cisco (past diet data are unavailable) but cisco are no longer available, then the fish may have resorted to extreme cannibalism of baby walleyes, the report said. The panel saw the theory as plausible, but we’ll never know for sure, said Venturelli, now employed at Ball State University in Indiana.

In fact, the Blue Ribbon Panel recommended the type of study just launched by Hansen. And its not too late for the research to shed light on how the less-productive food chain on Mille Lacs is affecting walleyes of all ages. The core problem is that baby walleyes are disappearing from the lake before they mature.

Hansen said her research group undoubtedly will want to keep the study alive into the next decade.

“Like most of the research I do, it leads to more questions,’’ she said.