This study describes for the first time metal accumulation in the eyes of native golden grey mullet (Liza aurata) coupled with water/sediment quality assessment. Sampling was performed in the Tagus estuary (Portugal) where a confined area (Barreiro) is severely contaminated by metal/loids. Levels of As, Cu, Pb, Hg and Cd in sediments from Barreiro were one order of magnitude higher than those from the reference site. Data on water column pointed also to a higher availability of Cu, Pb, Cd and Hg (including MeHg) at Barreiro. Accordingly, fish eyes accumulated higher levels of metal/loids at Barreiro than at the reference site. These findings support the use of fish eyes as a target organ in environmental health assessment since they reflect sediment and water contamination. It points also to the importance of evaluate eye changes at structural/functional levels in order to examine in what extent accumulated metals could compromise this perceptive system.