Southern flounder Paralichthys lethostigma is a recreationally and commercially important species along the western Atlantic and northern Gulf of Mexico coasts that can exhibit complex early-life habitat-use patterns. Herein, we used an otolith microchemical approach to test the conventional wisdom that juvenile southern flounder spend most of their early life in low-salinity areas of estuaries, focusing on the largely unstudied population in the Mobile-Tensaw Delta, AL. Analysis of strontium/ calcium concentrations in otolith cores of age 0 juveniles demonstrated that 68% of these individuals hatched in highsalinity waters before moving into freshwater habitats, with the remaining individuals being spawned in or near freshwater habitat. Further, otolith edge Sr/Ca concentrations revealed that even juveniles used freshwater habitats, particularly during freshwater/oligohaline conditions in our study system. Otolith edge Sr/Ca ratios for fish collected during high-salinity periods differed significantly among collection regions, suggesting seasonal differences in patterns of habitat use between individuals collected upstream (i.e., freshwater habitats) vs. downstream (i.e., euryhaline habitats). These data support the hypothesis that early-life stages of a substantial portion of a coastal southern flounder population use freshwater habitat.