Physiological biomarkers were compared in two estuarine fishes: an estuarine resident (Atherinella brasiliensis) and a marine/estuarine transient (Sphoeroides testudineus). These fish were sampled from two estuarine systems: one with an active harbor (impacted site), and another which receives mostly domestic urban runoffs and is much less impacted (reference site). The resident fish displayed higher plasma osmolality and sodium (1.13 and 1.35-fold, respectively), and the transient fish displayed higher plasma osmolality (1.05-fold), potassium (1.17-fold), and magnesium levels (1.84-fold) in the impacted site, when compared to the reference site. The resident fish showed increased renal carbonic anhydrase activity and branchial expression of HSP70 (3.3-fold) in the impacted site, when compared to the reference site. Osmoregulatory parameters and HSP70 expression are strong candidates as physiological biomarkers for environmental assessment of industrial impact on estuarine teleost fishes.