Mar 10, 2016

Winnebago System Muskellunge Management

An Often Overlooked Fishery

Adam Nickel, Wisconsin DNR Senior Fisheries and Winnebago System Gamefish Biologist

The Winnebago System boasts one of the largest naturally reproducing lake sturgeon populations in North America and one of the top walleye fisheries in the Midwest.  Therefore, it is not surprising that other species such as the muskellunge may be overlooked.  Angling pressure targeting muskellunge has increased on the system in recent years and reports indicate that anglers have been hooking into some trophy sized fish (> 50”).  As a result, local DNR staff members have been receiving more inquiries regarding the muskellunge fishery and many anglers are asking where these trophy sized fish are coming from.  Therefore, this article is intended to provide insight into the current status of the muskellunge population and the future direction of muskellunge management on the Winnebago System.

The Winnebago System has historically been home to a low density population of muskellunge.  The Great Lakes strain of muskellunge was once native to the Winnebago System; however, it is believed that the strain was extirpated during the 1900s due to various reasons including over-fishing and habitat degradation. Limited muskellunge stocking occurred during the 1970s, but the largest effort to bolster the population occurred during 2002-2007 when 613,248 Great Lakes spotted strain muskellunge (589,643 fry; 1,162 small fingerlings; 22,397 large fingerlings; 40 yearlings; and 6 adults) were stocked throughout the system.  The primary goals of these stocking strategies were to reintroduce Great Lakes strain muskellunge to the Winnebago System and potentially establish a naturally reproducing population. 

The Great Lakes strain muskellunge stocking program ceased on the Winnebago System in 2007 due to detection of the viral hemorrhagic septicemia (VHS) fish virus in the Winnebago System and Bay of Green Bay.  There is currently not an approved protocol in place for disinfecting cool water fish eggs from VHS positive waters.  Therefore, eggs taken from Green Bay fish can no longer be reared at state hatcheries, resulting in fewer fish available for stocking since 2007.  In recent years, three brood lakes have been established for Great Lakes strain muskellunge that could serve as a potential source for future stocking, but fish in those lakes still need time to reach sexual maturity.

Since the stocking events, DNR fisheries staff members have worked to track the Great Lakes strain muskellunge population.  However, relying on traditional sampling gear has been challenging considering the expansive area of the lakes and the diversity of habitat in the system.  As a result, DNR fisheries staff have applied an outside-the-box approach to sample the population that involves working with commercial rough fishermen.  The commercial fishermen bid on a contract that allows them to seine for rough fish (mainly common carp and buffalo) that are taken to market.  However, larger gamefish are also captured during seining efforts, which provides a great opportunity for DNR staff to collect biological data from a variety of gamefish species at a relatively low sampling cost.  Seining typically occurs during late fall when water temperatures are cooler to minimize the amount of stress on gamefish.  Effort is generally limited to one seine haul per year, but more hauls may be conducted if DNR staff desire to collect more data.

The length of the seine spans an impressive 8,700 feet and consists of 5 and 6 inch mesh panels.  The larger mesh size allows smaller non-target fish to go through the mesh, while retaining larger fish inside the seine.  Northern pike and muskellunge 30 inches and larger are retained by the gear as well, allowing DNR staff to collect needed biological data.  Other gamefish species including lake sturgeon, walleye, and flathead catfish are also collected during the survey.

The commercial fishermen begin by stringing out the seine, typically starting from Leonard’s Point and stretching the seine north across Lake Butte des Morts before looping back to the east and ending up back at Leonard’s Point.  The gear is estimated to sample an area of around 500 acres per seine haul.  The commercial fishermen then begin pulling the seine back into shore until the fish are congregated into a holding pen.  DNR fisheries staff are on site during this process to monitor the operation and process any gamefish that are captured in the seine.

Seining surveys have been conducted on Lake Butte des Morts in 2008, 2009, 2013, and 2014. Each captured fish is measured, weighed, and checked for a fin or maxillary clip from stocking events.  Three different markings were used to mark stocked muskellunge including a right maxillary clip, left ventral fin clip, and right ventral fin clip. Different combinations of marks were used to uniquely mark different cohorts of stocked fish, making it possible for fish to be tracked back to individual stocking events.  Any fish captured without a clip indicates that the fish was either from a fry stocking or naturally produced.  In addition to checking for fin clips, fish are also checked for Passive Integrated Transponder (PIT) tags and any untagged fish are then tagged.  Each PIT tag has a specific 10-15 digit alphanumeric code that is specific to that individual fish, which allows for information such as growth and movement patterns to be evaluated.

Size structure of Great Lakes spotted strain muskellunge captured during commercial seining surveys on Lake Butte des Morts in 2008 and 2009.Seining surveys in 2008 and 2009 captured 40 Great Lakes strain muskellunge ranging from 26.6-46.0 inches (average 40.2 inches; Figure 1).  DNR staff found that 37 of the 40 fish sampled were marked with maxillary or ventral fin clips indicating that they were from the small or large fingerling stockings during 2002-2007.  The other 3 fish sampled were likely from fry stocking events, suggesting that fingerling stockings were more effective than fry stockings.  Fin clip information also revealed that stocked fish were growing quickly.  For example, 4 fish ranging from 41.2-44.6 inches captured during the 2008 survey had left ventral fin clips that could be tracked backed to a 2002 large fingerling stocking event on the upper Fox River.  The recapture event indicates that stocked fish were reaching almost 45 inches in 7 summers of growth, thus it remained to be seen if these fish could top the 50 inch size range in the Winnebago System. 

There were 29 Great Lakes strain muskellunge captured during the 2013 and 2014 seining surveys, ranging in size from 38.9-51.7 inches (average of 45.3 inches; Figure 2).  Left ventral fin clips were observed on four of the larger fish sampled in 2014 (48.3, 50.0, 50.3, and 51.2 inches), which once again tracks back to a 2002 stocking event on the upper Fox River.  Therefore, fish in the system are reaching 50 inches in about 12 years of growth, which is well above the statewide average of 42.6 inches for 12-year-old muskellunge.  The 2014 seining survey also yielded the first PIT tag recapture of a Great Lakes strain muskellunge.  Tagging history of this fish indicates that the fish grew from 41.9” when originally tagged in 2009 to 49.0” when recaptured in 2014, which is quite impressive growth for a fish of this size. 

Although the size of fish sampled during the 2013 and 2014 surveys was impressive, the results demonstrate a shift toward an aging population.  For now the upriver lakes population appears to be dominated by larger fish from the 2002-2007 stocking events.  Although this is great for anglers today, the absence of fish less than 38 inches indicates a lack of new fish recruiting into the population. However, additional years may still be needed to allow for naturally produced fish to grow large enough to recruit to the mesh size of the seine.  Further, DNR staff conducted young of year (YOY) muskellunge electrofishing surveys on the upriver lakes and upper Fox River during the fall of 2015 and were unable to capture any YOY.  Only time will tell if signs of natural reproduction will appear, but the Great Lakes strain muskellunge population appears to be highly dependent on stocking at this point. Figure 2.  Size structure of Great Lakes spotted strain muskellunge captured during commercial seining surveys on Lake Butte des Morts in 2013 and 2014. 

Fortunately, Christmas came early during the summer of 2015 and the upriver lakes were stocked with 628 yearling Great Lake spotted muskellunge. Fish were dispersed between the upper Fox River (219), Lake Poygan (255), and Lake Butte des Morts (154).  All fish stocked in the upper Fox River and Lake Poygan were PIT tagged and received right ventral fin clips, while fish stocked in Lake Butte des Morts received right ventral fin clips only.  The 2015 stocking should help bolster population numbers and provide some future angling opportunities.   DNR staff plan to conduct additional fyke net, commercial seine, and YOY electrofishing surveys in 2016 to obtain more information about the current status of the muskellunge population and guide future management on the Winnebago System. 

Although often overlooked, the Winnebago System does currently offer some notable opportunities at landing a respectable sized muskellunge.  Anglers that hook into one on the system can bet that they are in for a great fight and there is a worthy chance that it could be a 50 plus inch giant.  Anglers can assist with Winnebago System muskellunge management by reporting lengths (if possible), capture location, and clips of any muskellunge caught.  Taking a quick picture of the fish is also encouraged so that the strain can be verified, particularly for fish less than 40 inches.  Sampling smaller immature fish with traditional gears and the seine can be difficult, thus it is important for DNR staff to know if anglers are finding some smaller fish while on the hunt for the fish of a lifetime.    

Thanks for taking the time to read this article and learn more about Winnebago System muskellunge management.  If you would like to receive email updates regarding Winnebago fisheries assessments contact me and we can add you to our email distribution list.  Also, remember to turn in walleye or yellow perch tag returns by either emailing to, mailing them to the Oshkosh DNR Office, or calling 920-303-5429.  Feel free to contact me by phone 920-424-3059 or email with any questions or to report your muskellunge catch on the Winnebago System.