A clean lake reflects well on all of us.



Adapted from: "Onondaga Lake Fishery: 2007-2008 Fact Sheet," by Onondaga County Department of Water Environment Protection, Sept 2008.

Onondaga County’s biological monitoring program tracks a number of plant and animal communities in the lake ecosystem. The monitoring program measures the number and types of fish, aquatic plants, macroinvertebrates, phytoplankton (algae), zooplankton, and zebra mussels. Results of the biological monitoring program are very encouraging; the lake now supports a diverse and productive biological community. Fish are quite abundant, and angling is becoming increasingly popular. Onondaga Lake now resembles other lakes of its size in the region with respect to the number of fish species, plant abundance, and summertime water clarity.

Species Present

The County’s monitoring program has captured forty-six different fish species since 2000. When combining the County’s species list with that of other recent studies, there have been sixty-six fish species identified in the lake in recent years. Fish species and their relative abundance are summarized in Table 1.

Table 1. Fish species documented in Onondaga Lake
Abundant Species
Alewife, Banded Killifish, Bluegill, Brown Bullhead, Carp, Channel Catfish, Gizzard Shad, Golden Shiner, Largemouth Bass, Pumpkinseed, Shorthead Redhorse, Smallmouth Bass, White Perch, White Sucker, Yellow Perch
Common Species
Black Crappie, Bluntnose Minnow, Bowfin, Brook Silverside, Brook Stickleback, Emerald Shiner, Fathead Minnow, Freshwater Drum, Longnose Gar, Logperch, Northern Pike, Rock Bass, Tessellated Darter, Tiger Musky, Walleye
Uncommon Species
Black Bullhead, Brown Trout, Goldfish, Greater Redhorse, Green Sunfish, Johnny Darter, Lake Sturgeon, Longnose Dace, Northern Hogsucker, Quillback, Rainbow Trout, Rudd, Spotfin Shiner and Trout Perch, White Bass, Yellow Bullhead

Origins of New Species

Quillback caught in Onondaga Lake as part of the
OCDWEP fish monitoring program.

In recent years several new species have been caught in Onondaga Lake
including lake sturgeon, quillback, green sunfish. and black bullhead. In some
cases these fish can be tracked directly to stocking efforts. For example,
because of identification tags on the fish, the lake sturgeon are known to have
made their way to Onondaga Lake from Oneida Lake where they had been
stocked as part of an effort to re-establish this endangered species. It appears
that other species may be naturally extending their range in New York.
Quillback (they resemble small carp but have a longer dorsal fin tip, see photo) are usually found in Lakes Ontario and Erie, not inland waters.

Several have now been captured in Onondaga Lake indicating that there is now
an established population here. Other species, such as the green sunfish and
black bullhead, are uncommon in most areas of New York and may have simply
avoided detection in the past. In all cases it is likely that new species are moving into Onondaga Lake via the extensive Seneca River system.

Lake Comparison

The number and kinds of fish found in any lake is dependent on several factors including quality of the water and physical habitat, lake size, and how intensively the lake is studied. Not many lakes are as well studied as Onondaga; so, comparable information is difficult to come by. We do know that Oneida Lake has a very diverse fish community and that sampling conducted by Cornell University has found over sixty species of fish, which is comparable to what has been found in Onondaga Lake.

Like most other nearby lakes, Onondaga Lake supports a very productive warm water fishery. Anglers from across the region, both recreational and professional, enjoy the lake’s excellent largemouth and smallmouth bass fishery. Numerous bass tournaments are held on the lake every year.

Reasons for the abundance of fish in Onondaga Lake are the connections between the lake and other regional waterways. Onondaga Lake is an open system, meaning that it is connected to other streams, rivers, and lakes with no barriers to fish passage. Ninemile Creek connects Otisco Lake to Onondaga Lake. The Lake's outlet flows north into the Seneca River that in turn is connected to the Finger Lakes, Oneida Lake, and Lake Ontario. Many fish likely enter the lake from the river and tributaries. For example, tiger musky stocked in Otisco Lake and brown trout stocked in streams connected to Onondaga Lake have moved downstream and been caught in Onondaga Lake.

Fish Consumption

Fish in Onondaga Lake have had elevated levels of mercury for many years. There is currently a health advisory issued by the NYS Department of Health to eat no largemouth or smallmouth bass over 15 inches, and no walleye, carp, channel catfish, and white perch of any size. The Department of Health advises up to four meals per month of Brown bullhead and pumpkinseed, and up to one meal per month of any species not listed. For additional information on fish consumption advisories in New York waters see the State report.


Onondaga County surveys anglers fishing on Onondaga Lake, the Seneca River (upstream and downstream of the lake), and Oneida River through the use of an Angler Diary Program. Fishing success in Onondaga Lake is typically comparable to, or slightly better than, fishing success in other local waters, including Oneida Lake (Figures 1 and 2). In general, smallmouth bass are more commonly caught in Onondaga Lake than largemouth bass. To participate in the angler diary program, please phone 315-435-2260 ext. 360, or click here.

Tagged Fish

As part of its ongoing monitoring, Onondaga County tags fish in Onondaga Lake with a yellow “spaghetti tag” below the dorsal fin. The information gathered from these tags, such as how far the fish moved and how much it has grown since it was tagged, is important in helping managers understand the fish community. Anyone catching a tagged fish should record the tag number, the length, weight, and location caught, and report this information to Onondaga County at 315-435-2260 ext. 360.

Fish Affect Lake

Alewives caught during gill net survey

The Lake's fishery can also affect the lake. This became all too clear in 2003 when a small fish called the alewife suddenly became very abundant in Onondaga Lake. This species feeds heavily on small lake animals called zooplankton and also on larvae of other fish. An important type of zooplankton was eradicated by the alewives. Since those zooplankton help clear the lake’s water by feeding on algae, the result was that water clarity actually declined. It appears that the alewives have also negatively affected reproduction of some fish species such as yellow perch and sunfish by feeding on their larvae. Onondaga County in cooperation with Cornell University will continue to monitor the effect of alewives on the Onondaga Lake food web.

Improvements in Fishery

With the improvements in the wastewater treatment processes at the Syracuse Metropolitan Treatment Plant (Metro), the fish community is improving, and more quickly than anticipated. The overall number of fish species caught in the lake has increased since comprehensive monitoring began in 2000. The abundance of many types of fish is increasing, including important game fish species such as largemouth and smallmouth bass (Figure 4).

Onondaga County uses data collected from the entire fish community to calculate what is called an Index of Biotic Integrity (or IBI for short) which measures the relative quality of the fish community over time. Figure 5 shows the results of this calculation, as a percent of the maximum possible value, since the year 2000. You can see that there have been subtle but steady improvements in the quality of the fish community since 2002.