Somatic growth rates, RNA:DNA, and feeding habits of juvenile Pseudopleuronectes americanus (Winter Flounder) were used to asses small-scale spatio-temporal variations in the habitat quality of Mount Hope Bay and Narragan-sett Bay, RI. Three successive caging experiments (14–16 d each) were conducted with flounder (initial size = 25–35 mm total length) in June and July 2003 in shallow water habitats (<1 m) of Spar Island, Common Fence Point, and Hog Island; the first two sites were located in Mount Hope Bay, and the latter in Narragansett Bay. The average growth rate of flounder ranged between 0.51 and 0.95 mm d⁻¹ and was inversely related with increased incidences of hypoxic conditions (i.e., amount of time dissolved oxygen was ≤ 4.0 mg L⁻¹). RNA:DNA, a surrogate measure of growth and feeding condition, corroborated somatic growth trends, and therefore exhibited similar spatio-temporal variability. In contrast to somatic growth, however, water temperature was the most important factor affecting flounder condition, such that RNA:DNA was inversely related to the amount of time water temperature was >20 °C. Benthic core samples indicated that food availability was greatest at Spar Island and was attributable to the numerical dominance of Crepidula fornicata Linnaeus (slipper limpet) during the early summer. Moreover, stomach contents of flounder reflected differences in prey species composition, whereby individuals from Spar Island consumed a higher percentage of molluscs relative to the other sites, where the preferred prey items were harpacticoid copepods and small decapods (primarily brachyuran crabs). Despite the observed discrepancies in feeding habits across sites, the extent of stomach fullness for flounder did not vary spatially (mean fullness = 44–49% across sites). It is concluded that the somatic growth, RNA:DNA, and feeding behavior of juvenile flounder in Mount Hope Bay and Narragansett Bay varies significantly across small spatio-temporal scales in response to changes in dissolved oxygen and thermal conditions.