Otoliths of cultured sea bass (Dicentrarchus labrax) from two different fish farms of Sicily were collected and analyzed by using inductively coupled plasma optical emission spectroscopy. Metal content (Ba, Cd, Fe, Mg, Mn, Sr, and Zn) was measured in order to test the potential use of biogenic carbonates as proxies of dissimilar environmental conditions since the fish farms are implanted in opposite coastal marine areas (Gulf of Castellammare and Gulf of Gela) characterized by different oceanographic features and human activities. Cluster analysis discriminates samples as different groups on the basis of metal content. Results show that concentrations of Sr in the otoliths have a similar range of distribution and not significantly different between the two farms. Otherwise, Fe, Mg, Mn, and Cd show higher concentrations in otoliths collected from fish reared in the farm in the southern coast (Gulf of Gela), an area subject to a great anthropogenic pressure. Zn is the only element with higher values in the otoliths from the farm in the northern coast (Gulf of Trappeto) probably due to industrial effluent. In this work, obtained data confirm the high potential of trace elements measurements in these biogenic carbonates as proxies of different environmental conditions.