The aim of the study was to evaluate the bioavailability of trace metals (Chromium, Copper, Nickel, Lead, Zinc, Cadmium, Arsenic, and Mercury) in the commercially consumed Crassostrea gigas oysters collected over a 12-month growth period (2011–12) from an experimental cultivation farm in La Pitahaya, Sinaloa State, Mexico. Sediment and water samples were also collected from four different zones adjacent to the cultivation area to identify the concentration patterns of metals. The results revealed that sewage disposals, fertilizers used for agricultural practices and shrimp culture are the major sources for the enrichment of certain toxic metals. The metal concentrations in oysters presented a decreasing order of abundance (all values in mg Kg−1): Zn (278.91 ± 93.03) > Cu (63.13 ± 31.72) > Cr (22.29 ± 30.23) > Cd (14.54 ± 4.28) > Ni (9.41 ± 11.33) > Pb (2.22 ± 1.33) > As (0.58 ± 0.91) > Hg (0.04 ± 0.06). Bioconcentration Factor (BCF) and Biota Sediment Accumulation Factor (BSAF) exhibited that C. gigas in the region are strong accumulators for Zn and Cd respectively. Thus, the present study proves to fulfill the gap in understanding the rate of bioaccumulation of metals in C. gigas which is regarded as the most sought after oyster species globally. Display omitted •Elevated metal levels in oyster species (C. gigas) from a cultivation site in SW Gulf of California Coast, Mexico.•High affinities of oyster to accumulate Zn and Cd from the ambient water and sediment fractions.•Impact of effluents from agriculture, aquaculture and domestic waste disposals.