Ontogenetic shifts in diet and habitat during the early life history of fishes can have a large influence on growth and subsequent survival. Considerable variation in body size at the end of the first year of growth is evident for southern flounder in North Carolina estuaries. Previous research suggests that age and settlement timing only contribute marginally to a ~2-fold difference in length at age-1. We hypothesize that the timing of ontogenetic shifts in diet and habitat may be largely responsible for observed growth variation in southern flounder. Biweekly sampling followed the 2018 southern flounder cohort each month. Stomach contents were used to quantify the occurrence of piscine prey. Muscle and liver tissues provided an analysis of 13C and 15N ratios to document habitat and trophic shifts over weeks to months. Otoliths were removed, sectioned, and examined to estimate growth rates in the most recent 30-45 d period. A controlled growth experiment in 2019 validated the assumed positive relationship between somatic growth and otolith growth. Muscle and liver tissues extracted from field sampling produced 13C signatures that largely differed between low and high salinity habitats, with only moderate overlap. Stomach contents and 15N tissue signatures documented an ontogenetic shift to piscivorous feeding that occurred at smaller body sizes within mesohaline habitats relative to fish found in oligohaline habitat. Otolith analysis revealed increased growth rates in flounder captured from mesohaline habitats that coincided with higher rates of piscivorous feeding.