The discharge of bleached kraft mill effluent (BKME) into Jackfish Bay, Lake Superior, Canada, has been associated with a number of changes in the physiology and whole organism responses of four fish species. Current studies have been following physiological indicators of BKME impact for evidence of improvement after the installation of a secondary treatment system. Secondary treatment has not been successful in eliminating BKME impacts on hepatic mixed‐function oxygenase (MFO) activity in white sucker (Catostomus commersoni) because fish collected from Jackfish Bay after initiation of secondary treatment exhibited similar MFO activity as recorded in samples collected during two previous years. Hepatic MFO activity was also induced in long‐nose sucker (Catostomus catostomus), lake whitefish (Coregonus clupeaformis), and lake trout (Salvelinus namaycush) after secondary treatment. However, samples collected two weeks after a planned mill maintenance shutdown showed no MFO induction in long‐nose sucker, reduced MFO activity in white sucker, and a reduced impact zone for MFO induction in lake whitefish. A reduction in circulating levels of gonadal sex steroids has also been recorded in fish exposed to primary‐treated BKME in Jackfish Bay. In contrast, neither secondary treatment nor mill shutdown was sucessful in eliminating impacts of BKME exposur on levels of testosterone and 17β‐estradiol in female white sucker and long‐nose sucker. The short duration of MFO induction after shutdown and the peristence of steroid reductions suggest that (a) secondary treatment has not been successful in removing “MFO‐active” compounds from BKME, (b) induction is not related to sediment contamination with persistent compounds, (c) the inducing agents are rapidly cleared by fish, and (d) effects on steroids may not be directly related to MFO induction.