Understanding the habitat preferences of juvenile fishes is critical for targeted management and conservation. Here, we examined juvenile abundances of Common Snook (Centropomus undecimalis) and Red Drum (Sciaenops ocellatus) across the major rivers of Tampa Bay, Florida (Alafia, Hillsborough, Little Manatee, and Manatee rivers) and related these to habitat connectivity, geomorphology, structure, vegetation, and water quality parameters spanning local-to-landscape scales. In 2019, 70 shoreline assessment sites were surveyed and paired with long-term fishery-independent monitoring records (1996–2023) filtered for early juvenile to sub-adult classes using seasonal and size criteria. Two negative binomial generalized linear models were developed for each species to identify predictors of abundance: one model focused on vegetation variables and the other focused on environmental variables. For Common Snook, abundance was significantly (p < 0.05) associated with salt marsh cover (+), proportion of organic matter in channel sediment (+) and shoreline sediment (+), canopy cover (–), woody debris cover (–), and water depths of the sampling location (+) and river channel (+). Common Snook abundance was also significantly influenced by river, with Hillsborough River supporting far fewer individuals. For Red Drum, abundance was significantly associated with mangrove cover (+), leafy debris cover (–), proportion of inorganic carbon in shoreline sediment (+), natural shoreline cover (+), outflow presence (+), water temperature (+), and salinity (+). Red Drum abundance was also significantly influenced by river, with Alafia River supporting far more individuals. These results underscore species-specific nursery habitat associations within a broader estuarine landscape and highlight the critical importance of conserving and restoring mangrove forests and salt marshes. Coastal wetlands are integral components of nursery habitat mosaics that support estuarine biodiversity and productivity, particularly amid increasing coastal development and climate change. Accordingly, restoration and management strategies should prioritize shoreline naturalization and the implementation of living shoreline approaches.