Stable isotope analysis has become a common tool for mapping trophic relationships, describing foodweb changes, and assessing ecosystem health. Clear interpretation of stable isotopes is facilitated by understanding how environmental factors can affect isotopic values; in estuarine systems, these factors may include salinity, land use, and shoreline habitat. To evaluate these factors, fish were collected from shallow-water habitats next to hardened (bulkhead and riprap) and unhardened (beach and marsh) shorelines within five subestuaries of the Chesapeake Bay that differed in predominant land use and salinity. This study focused on three common mid-Atlantic fish species: mummichog, Fundulus heteroclitus, Atlantic silverside, Menidia menidia, and white perch, Morone americana. Multiple regression analyses pointed to standard length, salinity, % of watershed as developed or crop land, and shoreline habitat type as important predictors for ?15N in all three species and for ?13C in mummichog and white perch. Further analysis controlling for the effects of salinity, land use, and fish size demonstrated that ?13C and ?15N were lower in tissues of fish collected next to marsh compared with hardened or beach habitat. Habitat effects were strongest for mummichog. This study focused on overarching patterns driving stable isotope signatures in fish; however, it also indicated potentially important interactions between nearshore habitat type and land use or salinity that deserve further analysis. Results have implications for the scale of isotope inquiry and give justification for more detailed follow-up studies of foodweb structure along modified and natural shorelines.