To test if otoliths can be used to track fish migration in polluted areas, fish sampled from Onondaga Lake, heavily polluted with mercury, were used in an assay to determine whether mercury was detectable in the fishes' otoliths using synchrotronbased scanning X-ray fluorescence microscopy (SXFM). Mercury was undetectable, but selenium, rarely reported in otoliths and known as a physiological antagonist to mercury, was. Strontium was also present but appeared to be taken up independently of selenium, and thus these serve as independent biogeochemical markers. Both selenium and mercury were detected in fish tissues, but selenium was below levels considered toxic. Selenium was low in otoliths of fishes collected in nearby Oneida Lake. Synoptic surveys of water chemistry revealed that Se is regionally highest in Onondaga Lake and in particular its main inlet, Onondaga Creek. SXFM appears to be a sensitive method for detecting selenium in otoliths.