Managing fish habitats by focusing on only one apparent habitat type, such as spawning sites, may mislead us by suggesting that, once protected, sites exhibiting high potential for egg deposition will eventually favour recruitment. Some supposedly high potential spawning sites may in fact exhibit low potential for population recruitment when considering their isolation to surrounding nurseries habitats. To maximize survival, post-hatched fish larvae need to access nurseries rapidly. Therefore, it is crucial to estimate precisely the connectivity between such key habitats. We quantified the probability of reaching nursery habitats for larvae of Northern pike (Esox lucius), a species using heterogeneous shallow habitats exposed to large water-level variations. The spatially explicit model developed for >130 km of the St. Lawrence R. allowed us to map the potential spawning and nursery habitats at high resolution. Using two software dedicated for the analysis of connectivity (Anaqualand, Chloe) we quantified spatial metrics, such as the number of sites, the surface of habitats, the proximity index, and the hydrographic distance. Preliminary results revealed a higher fragmentation within narrow sections of the river changing our interpretation of overall value for several presumed high potential spawning sites when considering their connectivity to neighboring nurseries. Habitat fragmentation leading to spatial separation of critical habitat during ontogeny could serve as a significant sink to recruitment.