In the early to late 1980s, water quality improvement and fisheries management facilitated the walleye population in the lake to reach approximately 40 to 70 million. In the late 1980s and through the 1990s, the walleye population began a decline that lasted for 10 to 15 years. It is thought that this decline was precipitated by a combination of over-fishing, environmental changes and the presence of invasive species. In order to stop this decline, the Lake Erie Commission (part of the Great Lakes Fishery Commission) set the total allowable catch for walleye at 3.4 million fish.

The introduction of non-indigenous species, such as zebra mussels and the round goby, to Lake Erie has reduced fish production and growth rates in many important fish species. As a result of zebra mussel invasion and phosphorous abatement programs nutrients have been decreased. This in turn, has reduced the amount of phytoplankton and resulted in shifts of the depth distribution of walleye.

Walleye spawning habitat has been lost through urban development, river barriers, and degradation of rivers by point and non-point source pollution, and have contributed to shifts in Lake Erie walleye capacity.