Until recently, Scott Finn didn’t bother fishing at Cottonmill Lake near Kearney. Really, few people did. There was no reason to, he said, unless you liked carp. “You could walk across the main part of it and not get your waist wet,” Finn said while casting for largemouth bass and northern pike one evening last summer.
Cottonmill Lake actually did hold largemouth, bluegills and catfish, but surveys by Nebraska Game and Parks Commission biologists showed there weren’t many, and those that were
present weren’t exactly fat and happy. There just wasn’t much for them to eat in the shallow, turbid waters. Carp, gizzard shad and other rough fish that called the lake home, on the other hand, were doing just fine, thank you.
That all changed in 1998, when Cottonmill became one of the first lakes restored under the Nebraska Game and Parks Commission’s Aquatic Habitat Program. Now Finn and other anglers flock to the lake and literally catch tons of fish. “I caught a lot of Master Anglers out here this year,” said Finn, referring to the awards the Commission presents to anglers who land trophy-sized fish. “I caught bass up to 6½ pounds, northern pike to 41 or 42 inches and catfish to 17 pounds. One day in mid-July I caught three 22-inch bass in 20 minutes.”
Hundreds of reservoirs of various sizes and shapes were built in Nebraska during the last century. From the 1920s to the 1980s, 145,000 surface acres of water were added to the state’s
inventory.
Previously, anglers were happy to fish the natural lakes in the Sandhills and the rivers and streams in their backyard. But they took a liking to these new waters, which were incredibly productive early in their life, and by the 1980s, 80 percent of all Nebraska anglers were fishing man-made lakes.
But whether they were built for flood control or irrigation, reservoirs weren’t designed to last forever. In fact, most of the flood control reservoirs in the eastern third of the state were designed to have a recreational life of only 100 years. In that time, sediment that washes in from the watershed or sloughs from the banks into the lake slowly but surely displaces the water until the lakes become nothing more than muck-filled marshes, still retaining their ability to hold back floodwaters, but little more.
By the late 1980s, “We were well past midlife on a lot of these waters and of course you could see it, too, in the condition of those reservoirs,” said Randy Winter, a Commission fisheries biologist who has led the Aquatic Habitat Program through most of its life.
Some older lakes had lost half of their volume to sediment, decreasing their depths to the point where winter fish kills were common. Many lakes were also dominated by undesirable fish species such as carp, which muddy the water, inhibiting the growth of aquatic vegetation. “You can’t grow quality largemouth bass and bluegill in a lake that doesn’t have a shred of aquatic vegetation and looks like chocolate milk,” said Winter.
As each decade passed, fewer new reservoirs were being built. The last big boom came in the 1970s, when several large flood-control reservoirs were built near Omaha. Most areas where dams could do the most good already held one. And societal values were changing: approval of each project became more difficult than the last because few people wanted to give up their land.
Until reservoir construction slowed, the fact that these fisheries were
declining wasn’t a concern to many. “It didn’t make any difference to anybody because they just moved to this brand new reservoir down the road that had great fishing in it,” Winter said. But fisheries biologists could plainly see the writing on the walls. “We had to take care of what we had or we weren’t going to have anything for the public to fish.”
Ben Nelson, then the state’s governor, said the public should decide which waterbodies should receive work, and that the plan must be approved by the Natural Resources and Appropriations committees. Public meetings were held, 91 water bodies were nominated and the top 17 were selected by Commission staff. The Natural Resources Committee didn’t approve the list, pointing to a lack of projects in Omaha, home to most of the state’s anglers. So biologists expanded it to 53 waters, including Cunningham Lake and ponds at Benson, Towl and Walnut Grove parks in Omaha. The plan was accepted, and biologists and engineers began designing projects.
The Aquatic Habitat Stamp became required for most anglers in 1997, and with that revenue, the heavy lifting of the program began. Anglers have since purchased more than 1.9 million stamps, and the $9.5 million generated has been leveraged against more than 70 other funding sources, most notably the Sport Fish Restoration Fund, Nebraska Environmental Trust, and Environmental Protection Agency program funds, providing more than $26 million for work to date.
The Solution
Vegetation
For many lakes in the Aquatic Habitat Program, restoring rooted aquatic vegetation, such as bulrushes, cattails, curly-leaf pond weed and arrowhead, is one of the primary goals. Vegetation provides a protected area for fish to spawn and a place for small fish to hide from big fish. It also provides a home for the aquatic organisms small fish eat. “All of those things contribute to the carrying capacity a lake has for certain species of fish like bluegill, black crappie and largemouth bass,” Winter said.

With improved water quality, cattails and great blue herons are now at home in Cottonmill Lake.
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Standards adopted long ago say that in order to have the best largemouth bass lake possible, 20 to 60 percent of the basin should be filled with aquatic vegetation, either the type that grows below the surface of the water or that extends above it. For bluegills, the optimum goal of vegetative cover is 20 to 80 percent.
“There’s quite a range there,” Winter said. “A lot of people will look at a lake and say ‘That’s too much vegetation,’ when really it’s just too much vegetation for anglers to fish. It’s not really too much vegetation for bass or bluegill.”
At Rock Creek Lake near Benkelman, water quality was good before an Aquatic Habitat Program project began there. Knowing work would make it even better and lead to an increase in aquatic vegetation, barriers were installed in 29 spots around the 50-acre lake that will inhibit plant growth and provide pockets of open water for anglers. As a bonus, this will increase the amount of “edge”
preferred by bass and redear sunfish.
In reality, it may be impossible to maintain adequate vegetative cover in some of Nebraska’s larger, windswept reservoirs. With that in mind, many aquatic habitat projects have included a modification of the lake’s outlet structure that allows water levels to be lowered periodically by up to three feet. In most cases, this will expose between 15 and 18 percent of the lake basin and give vegetation a chance to regenerate.
“What we can do is drop it down and expose the mud to sunshine and air so we can start getting cattails and bulrushes to grow,” Winter said. “Then when we fill it back up, we’ve got the vegetation we need to have a positive effect on bluegill, bass and crappie carrying capacity.”
When vegetation again declines, lake managers can repeat the process,
possibly every six to eight years.
Sediment
Vegetation won’t grow well, if at all, in mud-stained water, which is why removing sediment from reservoirs and then keeping it out is vital to the success of the program. Many lakes slated for Aquatic Habitat Program work must be deepened to ensure that fish have a place to go in the heat of the summer, when shallow water is too warm to support fish, and the dead of winter, when heavy ice cover can lead to low oxygen levels.
Reservoirs are typically drained to excavate sediment, allowing the soil to dry so heavy equipment can be used to scoop it out. When sediment is removed, a lake’s basin is typically sculpted to make it more fish-friendly than the fishbowl shape it often has become. The process is costly. Depending on where the silt can be disposed of, cost ranges from 65 cents to $7 per cubic yard.
Winter admits sedimentation is a case of good news, bad news. “If we hadn’t had erosion problems on farmland in the 40s, 50s and 60s, we wouldn’t have built a lot of these flood control reservoirs in the first place,” he said.
It wasn’t until after many of the reservoirs were built that people began to adopt techniques like contour and no-till farming and installing terraces, grassed waterways and buffer strips to help keep soil in the fields and out of the streams and reservoirs. Ensuring those practices are in place in the
watershed above a reservoir is now part of every Aquatic Habitat Program, thanks to the Natural Resources Conservation Service, Natural Resources Districts and Nebraska Department of Environmental Quality.
The biggest source of sediment flowing into some eastern Nebraska reservoirs, however, is not eroding farm fields, but construction sites in an expanding suburbia. A Department of Environmental Quality study found that while 20 to 30 tons per acre were being washed from some farm fields annually, 100 to 300 tons per acre were being washed from construction sites.
“There were about half a million cubic yards of sediment deposited in Holmes Lake from the time it was finished until the time we did the rehabilitation project,” said Winter. “We took out about half of it. We would’ve loved to have taken it all out but we didn’t have the money and didn’t have any place to go with it.” As it was, the 295,000 cubic yards of sediment removed from the Lincoln lake was piled on site, creating a mountain of sorts that would cover a football field 46 feet deep.

An Aquatic Habitat Project done on Holmes Lake in Lincoln so improved the water quality there that the lake bottom, ripe with aquatic vegetation, is now visible in this aerial photo, something unheard of before the work. The darkest areas are more than 10 feet deep.
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Because the watershed above Holmes Lake is almost completely developed, the amount of sediment flowing into the lake will be minimal in the future. But the amount of nutrients flowing into the lake could continue to be high. Most homeowners fertilize their lawns, and while an extensive education effort to encourage low phosphorous fertilizer use is underway, there is a vast amount of fertilizer flowing into that watershed. Streets, gutters and storm sewers carry those nutrients, as well as some of the waste deposited on lawns by the 13,000 dogs and cats that live above the lake, into the lake. Organic matter, be it leaves or grass clippings, will also continue to find its way into the lake. “Those nutrients have to go somewhere, and where they may go is into algae blooms,” Winter said. Like mud, algae can cloud water and inhibit the growth of vegetation in a lake.
Several wetlands in the Holmes Lake watershed will help filter some of those nutrients, including a series of five dams as well as some off-channel sediment basins on the main branch and a single, shallow wetland above the south arm of the lake.
Sediment and nutrient dikes or ponds built in feeder streams above a reservoir are another way to slow sedimentation. A two-stage sediment dike was built across the upper end of Wagon Train Lake near Hickman. The stream feeds the first cell, which traps the heaviest particles before water empties into the second cell, where aquatic vegetation filters more sediment and nutrients from the water before it flows into the lake.
The design has proven to be effective. Following a 2½-inch rain, the water in the main lake remained clear while the water in the upper cell was muddy. After a 5-inch rain, the entire lake was slightly muddy and took some time to clear, but that was expected, and much better than it would have been without the dikes. “You just can’t build anything big enough to deal with those kinds of runoff events,” Winter said. “You just have to live with that.”
The end result at Wagon Train is water clear enough to support sight-feeding predators such as walleye and muskellunge, which never would’ve fared well in the murky water the lake held before the project was done.
Mud isn’t the only type of sediment affecting the state’s reservoirs. At Rock Creek Lake near Benkelman and Grove Lake near Royal, the spring-fed streams flowing into the lake carry a considerable amount of sand – two tons per day from Verdigre Creek into Grove. While the sand doesn’t
necessarily affect water quality in the lake, it does displace a considerable amount of water. 19 percent of the surface area of Rock Creek Lake and 14 percent of Grove had turned from lake to marsh.
Rock Creek’s fishery was dominated by rough fish, so draining that lake for improvements was quite feasible. About 56,000 cubic yards of sediment were removed from the lake. At the upper end of the reservoir, a settling basin was dug behind a sediment trap to keep sand out of the lake. As necessary, the basin can be scooped out using nothing more than a backhoe.
Since Grove Lake still had a quality fishery, draining that lake for the work wasn’t an option. Instead, a hydraulic dredge was used to remove most of the sand and silt. To speed up the process, the lake was drawn down three feet in the winter when the ground was frozen, so backhoes could scoop off the top few feet of sediment and vegetation. Still, it took five years to remove 120,000 cubic yards of sediment.
Shoreline Protection
Windswept shorelines are susceptible to erosion. As the bank erodes and sloughs into the water, it decreases the slope of the lake bottom, making it easy for wind-driven waves to stir up the bottom. In smaller waters, vegetation is enough to stabilize shorelines. But in larger, windswept reservoirs, it takes hard engineering to protect them and keep vegetation growing.
Most aquatic habitat projects include jetties, islands or offshore breakwaters to protect the shoreline and create areas of calm water that are readily colonized by aquatic vegetation. These structures also increase the amount of shoreline, and therefore the amount of habitat available to fish. “For species like bass and bluegill, the more linear feet of shoreline you have for a given surface area of water, the more productive habitat you have for those species and the more pounds of those species you can produce,” said Winter. As a bonus, jetties also provide bank anglers access to fish preferring deeper water, including channel catfish.
Jetties built perpendicular to the shoreline can protect bays and part of the shoreline from crashing waves. They are, however, expensive to build, especially if built in standing water or if they extend a long distance into the lake. Dogleg jetties that run parallel to the shoreline for most of their length protect more shoreline and cost less.
The Commission plans on experimenting more with offshore breakwaters in future projects. A wave’s energy is distributed both above and below the water line. Waves pushed across a mile of open water by a 35 mph wind start stirring the bottom when they reach about 23/4 feet of water. A breakwater built in 4 feet of water with a height at or slightly above the water level will break these waves and prevent them from destroying the vegetation that will grow in the shallow, protected water behind them. Every 100 yards or so, jetties can be built connecting the breakwater to the shoreline for angler access and to protect these areas when wind blows parallel to the shoreline.
Breakwaters have been used at Branched Oak Lake near Lincoln, Olive Creek Lake near Kramer and Willow Creek Lake near Pierce. More are planned at Cunningham Lake in Omaha, which has been drained and where work will begin this winter.
These lakes are all small compared to the large irrigation reservoirs in western Nebraska. Vegetation isn’t as critical in irrigation reservoirs because most support a different type of fishery, primarily open-water species such as walleye and white bass. Yet shoreline erosion can still be a problem that is difficult to correct due to fluctuating water levels.
When Sherman Reservoir is full in the spring, crappies move into the shallow bays to spawn. “Because of all of the shoreline erosion and the lateral transport of that eroded material, a lot of these bays, especially the small ones, are getting cut off from the rest of the lake as they drop the water level for irrigation and a lot of our crappie spawn is being stranded up there and eventually dies,” Winter said. A series of jetties and offshore breakwaters will protect those bays when the lake is full, helping improve the fishery, even though they will spend part of the year out of the water. A few are complete and more will be built this year.
The breakwaters are expected to hold some water behind them when lake
levels fall, encouraging the growth of willows and other vegetation that will serve as additional spawning habitat for crappies when the lake refills. The rock structures will also provide additional spawning habitat for walleyes.
Another technique biologists are experimenting with is called a groin, a windrow of rocks running into the lake from the high-water mark, perpendicular to the shore, that also helps stop the lateral movement of sediment.
Bad Fish
The fish community in older lakes that suffer from poor water quality and have little aquatic vegetation is typically dominated by carp, gizzard shad, white perch or other rough fish. Bottom-feeding carp muddy the water. Shad and white perch compete with sport fish for food.
Unless these fish are removed from both the lake and its watershed, sport fish have little chance of flourishing. That typically means killing all fish with rotenone, a short-lived toxicant. By starting from scratch, sport fish that are stocked following a project have a chance to gain a foothold in the lake and can typically control most rough fish that happen to find their way back into the lake.
“It isn’t the same as when you can see a nice big fishing jetty or breakwater, but if you get rid of the carp, it allows nature to improve the habitat,” said Joel Klammer, district fisheries supervisor in the Commission’s Basset office. “It cleans up the water clarity and you get the vegetation coming back along with lots of plankton and that is good for ducks and fish.”
Cottonwood, Steverson and Home Valley lakes, all located on Cottonwood-Steverson WMA north of Hyannis, are examples of this work. The three lakes were dominated by carp. In 1998, soon after they were purchased by the Commission, they were renovated with rotenone and restocked, and now provide quality fishing for walleye, largemouth bass and muskellunge.
So important is removing undesirable fish that the process was completed twice at Wagon Train Lake. Work was done and the lake was restocked with bass and bluegills and had begun to refill. But when biologists found carp in the lake, they killed off the fishery again. They also sampled each of the more than 20 ponds in the watershed until they found the source of the carp, and removed those fish as well.

Aquatic vegetation can now be found throughout much of Wagon Train Lake, especially in areas protected by jetties which also provide anglers easy access to deep water.
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Keeping rough fish out of lakes isn’t always easy. During wet periods, natural lakes and sandpits can connect to other lakes or streams, bringing in more carp and setting the stage for more trouble. This was the case with Goose Lake south of O’Neill, which connects to the Elkhorn River when water is high.
To combat the problem, porous rock barriers were built across the four low areas that connected Goose Lake to the streams. Similar structures may be a part of any future renovations on natural lakes, including Crescent Lake north of Oshkosh, a public lake that so far has no public access but will hopefully be a part of the Aquatic Habitat Program in the future.
Rough fish sometimes are reintroduced to a water body by an angler who dumps his minnow bucket into the water following a day’s fishing, not knowing that one of those minnows is actually a carp. For that reason, live baitfish are banned at most lakes where aquatic habitat work has been completed. “There are a lot of users on those lakes and a lot of chances for people to screw it up by putting fish in there that shouldn’t be there,” said Jeff Jackson, district fisheries biologist in the Commission’s Lincoln office.
Jackson was referring to what staff like to call “bucket biologists,” individuals who move their favorite fish from one lake to another. Some like to move crappies. This popular panfish is capable of producing a huge year class of fish in a restored lake. “The crappies can then tie up the biomass and you wouldn’t get the high bass density you want because the crappies will actually prey on small bass,” Jackson said. “That will put a lake out of balance right away.” If crappies are stocked before bass become well established, problems can result. If they are stocked after high bass densities develop, good crappie populations can result.
Jackson likes to see these high bass densities in the lakes he manages shortly after a project is completed. Largemouth bass, native to Nebraska, create the highest predator densities and best control in waters less than 750 acres. Predators such as bass, walleye and muskie can control carp and
bullheads, but not white perch and gizzard shad. “I don’t know of any predator that biologically controls those two species,” Winter said.
What’s Next
Nebraska was the first state in the country to have an official program to improve aquatic habitat with a dedicated funding source. But the Commission, as well as other resource management agencies around the country, had already been working to improve reservoirs, lakes and streams. And project planners have learned a few things along the way and a few since.
Not all of the projects have been successful. Harkreader’s Pond at Lake Maloney showed great promise, but a leak in the pond has forced managers to pump groundwater to maintain the water level, and even that has met with limited success. At Shell Lake near Gordon, sediment may have shifted and filled in the area deepened using a hydraulic dredge. And aeration projects, designed to expand habitable water for fish in sandpits where deep water lacked oxygen, didn’t always improve a fishery.
Even Cottonmill Lake has its problems. A sand filter system designed to remove rough fish from the canal water used to fill the lake continuously plugged up with mud and failed. Now water must be filtered through a larger screen, which could allow rough fish in the larval stage to pass through. As a result, water levels in the lake remain a few feet below what was originally planned.
Of the 53 scheduled projects, 41 are complete and eight more are in progress. Three sandpits at Fremont Lakes State Recreation Area were dropped from the plan after biologists realized they couldn’t make measurable improvements to them. Additional work at Branched Oak Lake is on hold and may never come to fruition. Making a significant dent in the problems there would require draining the lake, an idea that’s not popular among the one million people who visit it each year, and would also be costly. It was expected the initial list of projects could be completed in 10 years, but it could take 15 years. “We didn’t know how long it was going to take to do this stuff,” Winter said. “No one had ever done it before, so we had no idea how long it would take or how much money it was going to cost.”
But biologists are already starting to plan for round two of the program and there are plenty of candidates for the new list. While coldwater streams didn’t rank high enough on anglers’ priority lists in round one, several in the North Platte River Valley and in north-central Nebraska are good candidates for this second round. Once biologists put together a list they feel is both
feasible and would provide the most bang for the buck, they will go to the public and make their case for those projects.
Mission Accomplished
Winter thinks the work has been well worth the effort. “I think some astute fisheries guy could say ‘I can produce just as good a fishery in Wagon Train without having to spend all of that money by simply draining it, killing out whatever fish were left in it, refilling it and restocking it,’” Winter said. “And he wouldn’t be wrong. The difference is he can’t sustain it as long because of all the improvements we’ve made.
“Our consultants estimated we probably added 60 or 70 years to the recreational life of Wagon Train and we’ve added 85 years to the recreational life of Holmes Lake. You think about that. There’s going to be two or three more generations that will be able to enjoy those two waters that wouldn’t have been be able to otherwise. Then somebody else will come along later and redo what we’re doing and maybe even do it better.”

Mason roz ties on another lure as David Neimeyer, Isaac Mitchell, Noah Murrish, Logan Berck and Bailey Block, all members of the New Life Assembly's Royal Rangers youth group, fish from a jetty at Cottonmill Lake in Kearney.
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Cottonmill Lake is a prime example of what can be done to restore a lake. Built in 1886 to provide power for the cottonmill factory, the lake had so silted in that winterkills of fish were common. Its maximum depth was 4 feet and its average depth was between 2 and 3 feet. “It was about as poor as you can get for a 40-acre reservoir,” said Brad Newcomb, district fisheries manager in the Commission’s Kearney office. “It can’t get much worse than that.” The lake was drained and about 150,000 cubic yards of muck was removed from its bottom, enough to cover a football field 23 feet deep.
In the process, the volume of the lake was increased from 81-acre feet (an acre-foot of water covers an acre, about the size of a football field, with a foot of water) to 181-acre feet. The
maximum depth of the lake was increased to 18 feet, and a good portion of the lake is now more than 10 feet deep, the magic number biologists shoot for to avoid winterkill. Plus, two islands, two hard points, an offshore breakwater and four jetties were built to protect the shoreline from wave
erosion. Combined, the structures added 4,100 feet of shoreline to the lake, a 30 percent increase.
Unlike most reservoirs, Cottonmill is not fed by a stream. Instead, water is delivered through the Kearney Canal. Because of that, Newcomb said, the lake doesn’t have the problems other waters do following heavy rains in the watershed, namely huge flushes of sediment followed by a period of cloudy water.
“It had a lot of potential,” Newcomb said.
Work was completed in 1998 and after the remaining fish in the lake were killed, it was restocked in 1999 with bass, bluegill, black crappies, channel catfish and northern pike.
The clarity of the lake’s water has improved from poor to excellent thanks to the project. At times, the lake bottom is visible in 10 feet of water. “With clear water, the aquatic vegetation is super and the fish habitat is excellent,” Newcomb said, pointing to the
vegetation that rings the lake.
Anglers and fish are both taking full advantage of the project. During May and June of 1993 and 2006, anglers were surveyed during specific time periods. In 1993, the creel clerk found a scant 11 anglers at the lake during the selected times. In 2006, the number of anglers had exploded, with the creel clerks surveying 454 anglers from 14 counties and two other states.
Based on those interviews, it is estimated that in 1993, 394 anglers spent a total of 503 hours at Cottonmill during May and June and caught a total of 521 fish. In 2006, there were
exponential increases on all fronts, with an estimated 5,561 anglers spending 11,122 hours fishing the lake. Their total catch: a few more than 18,000 fish, including 11,349 bluegills and 5,187 bass.
“It’s a pretty remarkable comparison,” said Newcomb.
And one that anglers like Scott Finn will appreciate, for the most part. “On Memorial Day, I dragged my girlfriend down to the bait shop and made her buy a fishing license,” he said. “Ninety minutes later she caught a 40-inch pike. Now I’ve got to sneak out the door.”