Many of Wisconsin's native populations of muskellunge Esox masquinongy exhibit declining reproductive success and failing natural recruitment. As a result, self‐sustaining populations of muskellunge are diminishing. This study focused on spawning habitat factors that influence egg development and survival and, consequently, the reproductive success of muskellunge. Muskellunge spawning habitat characteristics in lakes with self‐sustaining populations were compared with spawning habitat characteristics in lakes that were once self‐sustaining but are now maintained by stocking. The hatching success of artificially fertilized eggs was assessed under natural lake conditions. Spawning sites were typically marshy areas in water less than 1 m deep. Characteristics of the spawning habitat influenced successful reproduction. Spawning areas in stocked lakes had low dissolved oxygen (DO; 1.2–5.4 mg/L) at the substrate–water interface, whereas self‐sustaining lakes had more variable DO (0.5–9.6 mg/L) with some microhabitats having high DO. Organic carbon content, texture of spawning substrate, and water temperature at the substrate did not differ between self‐sustaining lakes and lakes supported by stocking. Fallen logs, stumps, and other wood in spawning areas may increase egg survival. Muskellunge egg survival over natural substrate was low (0.0–1.3%), even in lakes with self‐sustaining populations. Collections of eggs and observations of fry indicated that major mortality occurred after egg deposition but before fry reached nursery habitats several weeks after hatching.