The aim of this study was to evaluate Fe and Mn distribution in geochemical fractions of the surface sediment of four oyster culture sites in the Sonora coast, Mexico. A selective fractionation scheme to obtain five fractions was adapted for the microwave system. Surface sediments were analyzed for carbonates, organic matter contents, and Fe and Mn in geochemical fractions. The bulk concentrations of Fe ranged from 10,506 to 21,918 mg/kg (dry weight, dry wt), and the bulk concentrations of Mn ranged from 185.1 to 315.9 mg/kg (dry wt) in sediments, which was low and considered as non-polluted in all of the sites. The fractionation study indicated that the major geochemical phases for the metals were the residual, as well as the Fe and Mn oxide fractions. The concentrations of metals in the geochemical fractions had the following order: residual >> Fe and Mn oxides > organic matter > carbonates > interchangeable. Most of the Fe and Mn were linked to the residual fraction. Among non-residual fractions, high percentages of Fe and Mn were linked to Fe and Mn oxides. The enrichment factors (EFs) for the two metals were similar in the four studied coasts, and the levels of Fe and Mn are interpreted as non-enrichment (EF < 1) because the metals concentrations were within the baseline concentrations. According to the environmental risk assessment codes, Fe and Mn posed no risk and low risk, respectively. Although the concentrations of Fe and Mn were linked to the residual fraction, the levels in non-residual fractions may significantly result in the transference of other metals, depending on several physico-chemical and biological factors.