ABSTRACT: Biological and environmental conditions are drivers of fish habitat use, making it essential to understand how fish move and use specific areas to inform effective fisheries management and conservation. This study quantified the residency and habitat use patterns of the juveniles and early adults of two commercially exploited snappers (Lutjanidae) in Santa Elena Bay, a tropical estuarine embayment influenced by a seasonal upwelling in the north Pacific coast of Costa Rica. Using an array of 28 acoustic receivers we monitored 14 Colorado (Lutjanus colorado; 28.8-48.9cm) and 16 Pacific dog (L. novemfasciatus; 22.5-49.3cm) snappers over 22 months. Both species were detected inside the bay over 60% of the monitoring days, showing higher relative abundance in mangrove and transitional estuarine habitats. Throughout the study, a shift in habitat use was observed for both species. Individuals moved from mangrove and transitional habitats to the outer reef habitat, and exhibited a decreasing occurrence probability over time, suggesting they leave the bay as they mature. Season and environmental variables, e.g. temperature, had minimal or no effect on the occurrence of the tracked snappers in the bay. However, roaming varied seasonally, increasing during upwelling periods. These results suggest that habitat connectivity facilitates gradual life stage transitions, indicating that Santa Elena Bay likely supports essential fish habitat for commercially important species, particularly for L. novemfasciatus. Results also highlight the importance of integrating knowledge of the complex interplay of biological components (e.g. developmental and intra and interspecific interactions) and seasonal habitat dynamics into conservation and management strategies.