Isotopic ratios of fish otoliths have been used in numerous studies as natural tags or markers to aid in the study of connectivity among fish populations. We investigated the use of spatial and temporal changes in the stable carbon and oxygen isotope ratios of otoliths to differentiate juvenile habitats of winter flounder (Pseudopleuronectes americanus). Young-of-the-year (YOY) juvenile winter flounder were collected annually over a three-year period from 18 stations along the coast of Rhode Island, USA. Sagittal otoliths were removed from fish and analyzed for stable carbon ( 13 C/ 12 C or δ 13 C) and oxygen ( 18 O/ 16 O or δ 18 O) isotope ratios using continuous flow isotope ratio mass spectrometry. Differences in isotope ratios were observed among stations and along salinity gradients in the Narragansett Bay estuary and an estuarine river system (Narrow River). Overall, the isotope ratio patterns observed among stations were consistent over the three sampling years; however, differences were noted in isotope ratios and the magnitude of the isotope ratio gradients among years. Significant positive correlations were noted between salinity and δ 13 C for two of the three years. For each of the three years sampled there was a highly significant positive correlation (2002, r= 0.93, P<0.01; 2003, r=0.85, P<0.01; 2004, r=0.97, P < 0.01) between δ 18 O and the salinity of the collection site. Also, there was a significant negative correlation between the number of months of above average river flow and δ 18 O for the three sampling years (r=0.99, P<0.05). These findings suggest that yearly changes in the volume of freshwater inputs to these estuarine habitats may be related to the differences observed in otolith δ 18 O isotope ratios. Because of these year-to-year differences, sampling of each cohort may be necessary in order to use this isotopic technique for winter flounder connectivity studies.