Territorial Parma microlepis (Gunther) (Pomacentridae) were collected at different depths, at three sites in each of four estuaries near Sydney, Australia. Element concentrations were measured by induc- tively-coupled–plasma mass spectrometry. Significant differences in concentrations of Mn and Ba were found in the otoliths of fish sampled in different depth strata, with concentrations generally greatest in fish found in water <4 m deep. Depth-related differences varied among estuaries (e.g. 0 to 1.2 μg Ba g−1 otolith). In most estuaries there was a negative linear relationship between concentrations of Mn and Ba in otoliths and actual depth. Great variation was found within an estuary among sites separated by 0.5 to 3 km. In the eye lenses, concentrations of Rb differed according to depth of capture of fish. The age of fish (1+ to 34 yr) had no influence on the concentrations of elements in otoliths or lenses. Multivariate comparisons of elemental composition (= fingerprints) detected significant differences among depth strata. Fish collected from shallow water had the clearest multivariate classification according to depth. There was a close match between our shallow strata and the average depths reached by low-salinity/high-temperature estuarine plumes. The element composition of whole otoliths and lenses represents average concentrations experienced by the fish. The temporal resolution of differences in ambient conditions is likely to be coarse in the fish (i.e. months to years).