Walleye (Sander vitreus) is an important sport fish in the Great Lakes that is experiencing low reproductive success after severe population declines starting in the late 1940s. In the Muskegon River, Michigan, natural reproduction of walleyes remains low and is largely supplemented by stocking. To determine factors influencing walleye reproductive success in the Muskegon River, we estimated walleye egg survival using in situ egg incubators covered with nitex screening (2003–2004) and estimated density and survival of fertilized eggs caught on furnace filter traps across different substrate types (2005–2006). We compared physical habitat suitability for walleye eggs under high and low flow scenarios. Density of walleye eggs was highest in regions of gravel/cobble substrates. Egg survival was higher in egg incubators (24–49.5%) than on furnace filter traps (2.0%), suggesting predation is an important source of walleye egg mortality in the Muskegon River. Cold water temperatures that extended developmental stage durations may also be an important source of egg mortality. The dynamic habitat suitability model predicted low suitability for eggs due to poor temperature and velocity conditions. Despite low egg survival rates, 40 million to 1 billion eggs were estimated to hatch. The low natural reproduction of walleyes in the Muskegon River is likely due to a combination of low walleye egg survival and failure of walleye larvae to reach their nursery grounds in Muskegon Lake.