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Juvenile organisms often shift habitat usage during ontogeny to balance changing needs for growth and refuge, yet fine-scale habitat shifts within narrow size classes remain understudied. We conducted a manipulative tethering experiment to quantify size-specific survival of juvenile blue crabs ( Callinectes sapidus ) across three habitats – seagrass meadows (seagrass), salt marsh edge (SME), and unvegetated sand flats (sand) – in the York River, Chesapeake Bay, USA. We also accounted for spatial orientation, seasonality, and turbidity. Results were analyzed using Bayesian hierarchical logistic regression models. Survival varied with crab size, habitat, and time of year, with an interaction between size and habitat. Smaller juveniles had the highest survival in seagrass, but survival increased more rapidly with size in SME and sand habitats. By 33 mm carapace width (CW), relative survival rates in seagrass and SME were statistically indistinguishable. Meanwhile, survival in sand approached that of seagrass at approximately 45 mm CW. When considered alongside previous growth rate studies, these results suggest that seagrass offers a growth–survival advantage for crabs < 15–20 mm CW, while salt marsh and sand habitats become increasingly favorable for larger juveniles due to comparable survival and faster growth. Consequently, even across a relatively small size range of the juvenile phase, size-specific patterns in survival differ substantially across structured and unstructured habitats. Our findings align with observed patterns of size-specific habitat use and underscore the complementary nursery roles of seagrass and salt marshes, reinforcing their joint importance in habitat restoration and conservation strategies for juvenile blue crabs.