Spawning and nursery habitats are often spatially disjunct as a consequence of specific life history stage habitat requirements and spatiotemporal habitat changes. Nevertheless, free‐swimming larvae originating from spawning habitats must reach productive nurseries to maximize survival. We examined spawning and nursery habitats of northern pike (Esox lucius) over the past 50 yr to investigate how habitat connectivity and hydrological variability interact to alter the distribution of effective spawning habitat. Habitat models coupled to a least‐cost approach were developed to quantify connectivity between habitats in two contrasting regions of the St. Lawrence River (Canada): a riverine corridor lake (~ 46 km) and a large fluvial lake (~ 48 km). Our simulations demonstrate that depending on hydrological conditions, between 3% to 51% of spawning habitat used by adults in the riverine corridor, and 22% to 90% in the lake, allowed larval survival up to the fifth week of development. Although rapid dewatering of spawning habitat is responsible for most spawning losses in the fluvial lake, increasing water currents were responsible for dispersing larvae away from suitable habitats in the riverine corridor. However, stable hydrological conditions led to spatial overlapping of spawning and nursery habitats favoring larval survival and growth. In addition, downstream larval dispersal by low water currents allowed larvae to reach spatially disjunct nursery habitat, especially in the lake. Our results indicate that despite the vast areas of potentially suitable habitats provided by large vegetated floodplains of fluvial lakes, the effective spawning habitats favoring early‐life recruitment are much more heterogeneous and variable both spatially and temporally.