The present study aimed to determine trace elements in Mediterranean mussels (Mytilus galloprovincialis) from an experimental pilot farm of the Calich Lagoon, a typical Sardinian brackish area (Italy). Two sampling sessions were scheduled in February and May 2019 and the occurrence of 24 metals (Hg, Ag, Al, As, Be, Bi, Cd, Co, Cr, Cu, Fe, Ga, In, Mg, Mn, Mo, Ni, Pb, Rb, Se, Sn, Ti, V, Zn) in bivalves was considered. Environmental conditions of water (temperature, salinity, pH, dissolved oxygen, and chlorophyll a) were also measured in situ. A high significant (P<0.001) difference was reported for temperature, pH, and dissolved oxygen. Our results showed a significant sessional variation of Mo (P<0.001); Cd, V (P<0.01); Ni, Pb and Co (P<0.05) in examined M. galloprovincialis samples; as all values were higher in February than those for May session samples, meanwhile the highest levels were reported for Mg (mean s.d. 1151 263 mg kg-1 wet weight), Al (mean s.d. 341 192 mg kg-1 w.w.), and Fe (mean s.d. 212 75 mg kg-1 w.w.) in February samples. The European Union uppermost values (EC Reg. 1881/2006) for Cd, Hg, and Pb were never overpassed. The results confirmed the role of M. galloprovincialis as one of the most appropriate biological indexes to track the presence of trace elements in brackish environments. It could be concluded that the current ecology of the Calich Lagoon suggests that compatibly with the transitional ecosystem, the classification as a bivalves’ production area and the implementation of extensive shellfish farming can improve its production capacities. The knowledge of the lagoon ecology is an essential tool for its sustainable exploitation, preserving biodiversity, and mitigating the effects of anthropogenic activities on public health.