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The St. Lawrence estuary (SLE) supports important nursery habitats for many fish species, including the newly re-established population of striped bass (Morone saxatilis). The present study aims to describe pelagic (5 m isobaths) and littoral (<1.5 m-deep) nearshore habitats of the SLE and to document their use by fish larvae and age-0 juveniles, especially for striped bass. From June to September 2014, 162 pelagic and 188 littoral stations were characterized in terms of biophysical conditions (turbidity, salinity, temperature, dissolved oxygen and chlorophyll- a concentration), abundance of main preys and fish assemblages. Striped bass larvae identification was confirmed with genetic analyses. In the pelagic and littoral zones, four estuarine habitats were defined based on turbidity and salinity: an upstream freshwater section (UP), an oligohaline (O-ETM) and a mesohaline (M-ETM) estuarine turbidity maximum zone, and a downstream polyhaline section (DOWN). Our results emphasized the spatial partitioning of fish early life stages among contrasting habitats, potentially to minimize interspecific competition. In the SLE, striped bass is using the wide spectrum of habitats available. At the onset of striped bass development, the UP and the O-ETM were the main nursery habitats, which is consistent with the known location of spawning grounds. Results suggest that the O-ETM provided the most suitable conditions for the species with optimal physical properties and abundant food resources. Later in the season, the M-ETM provided a favourable trade-off habitat offering a less optimal physical environment although potential for new prey. • Along de salinity gradient, four distinct estuarine habitats were identified in the St. Lawrence Estuary. • Contrasting habitats support distinct assemblage of fish early life stages along the salinity gradient. • Along the growing season, striped bass (Morone saxatilis) is using the wide spectrum of habitats available. • The O-ETM provided the most suitable conditions for striped bass with optimal physical properties and abundant food resources. • The dispersion of striped bass further downstream may be a mechanism to partition the estuary, and to minimize competition. [ABSTRACT FROM AUTHOR]