The Saginaw Bay watershed is the largest drainage basin in Michigan, draining approximately 15% of the total land area.

The first to visit the Saginaw Bay area was Father Jacques Marquette, a French Jesuit missionary priest, who went there in 1668 after establishing a mission in St. Ignace.

In 1686, Father Jean Enjalran [fr] arrived in the valley to establish an Indian mission, but his efforts failed.

During development of natural resources in the 19th century, Saginaw Bay was busy with shipping of lumber and other commodities to eastern markets.

This was attributed mainly to habitat degradation (dam construction, sedimentation of off shore spawning areas), pollution, cultural eutrophication, and the effects of invasive species.

The walleye fishery began a resurgence in the early 1980s when the Michigan Department of Natural Resources initiated a fingerling stocking program.

Alewives used Saginaw Bay's near-shore waters as spawning and nursery grounds and were a formidable predator and competitor on newly hatched percid (walleye and yellow perch) fry.

The Michigan Department of Natural Resources discontinued stocking in 2006, and walleye recovery targets were formally met in 2009.

Although yellow perch also benefitted from the absence of alewives with greater reproductive success, the numbers of adults has declined and remained depressed.

A cisco fingerling stocking program aimed at restoring a breeding population in the bay was initiated in 2017, a joint exercise by the U.S.

Fish and Wildlife Service, the Michigan Department of Natural Resources and other partner agencies of the Great Lakes Fishery Commission.