Coastal lagoons are known to host numerous resident and migrant fish species. Spatio-temporal variation in abiotic and biotic conditions in these ecosystems results, however, in a mosaic of microhabitats that could differently affect juvenile growth and survival. To deepen our understanding of juvenile fish habitat requirements and their spatio-temporal use of lagoons, microhabitat characteristics and fish assemblages were monitored jointly in a small temperate lagoon (the Prévost lagoon), from March to October 2019. A total of 2206 juvenile fishes belonging to 22 species were collected. Resident lagoon species, especially Atherina boyeri, dominated the assemblage (74%), while, among migrant species, Sparus aurata (8%) and Liza aurata (5%) were the most represented. Changes in overall juvenile abundance were mainly temporal, following the seasonal shifts in water temperature, salinity, and chlorophyll a concentration (44.9% of the co-inertia). However, our results revealed that distinct types of microhabitats exist in small lagoons and that juvenile fish distribution among them is non-random. Indeed, fish species richness mainly differed among sampling sites in relation to their distance from the inlet and the complexity of the three-dimensional habitat structure (36.5% of the co-inertia). Juveniles preferentially selected microhabitats with medium to high structural complexity, which were essentially created by macroalgae. However, microhabitat preferences were both species and ontogenetic stage dependent, with more contrasting microhabitat requirements in young juveniles. These results underline the need for conservation measures to consider each lagoon as a dynamic mosaic of microhabitats with radically different importance for the juveniles of the various fish species that colonize them.