Trace element (Fe, Mn, Cr, Cu, Ni, Co, Pb, Zn, Cd, As, Hg) concentrations were assessed in marine organisms (n = 52) sampled from the Magdalena Bay lagoon complex in Baja California Sur, Mexico, a pristine marine environment. The overall trend of metal concentrations (dry weight) in the organisms was found to be Fe[Zn[Cd[Cu[ Mn[Pb[As[Hg[Ni[Cr[Co. Bivalve mollusks (53.83 mg kg-1) contained twofold higher levels of metals than the finfishes (20.77 mg kg-1). Calculated BioConcentration Factor (BCF) values showed that dissolved Mn is readily bioavailable to the organisms, whereas Biota Sediment Accumulation Factor (BSAF) indicated high values for Zn, Cu and Cd. Cd and As levels were observed to be increasing with the trophic levels. Toxic elements, namely Pb, Cd and As in the studied fish species were found to be higher than the values recommended for human seafood consumption. The study provides a comprehensive baseline report on trace element bioaccumulation in several marine organisms that will aid in developing effective conservation strategies of the highly biodiverse lagoon complex.