Geochemical analysis of Crassostrea cucullata shells was carried out to study the pollution of the Iraqi aquatic brackish and marine environments. Samples of shells and water were collected from the intertidal zone at seven different stations (Fadakia, Rass Al Bishah, Khor Abdullah, Khor Shytianah, Hacham Island, Khor Al Zubair, and Shatt Al Basra) during low tide period from March to August 2011 from the Shatt Al-Arab, Shatt Al-Basra and Iraqi coasts along the North Arabian Gulf. The hydrochemical analysis reflects three zones of water salinity, Fadakia and Shatt Al Basra of Brackish water with total dissolve solid (TDS) range (15,148–18,130 ppm), Rass Al Bishah of saline water with TDS range (34,123–36,521 ppm), and the other marine coastal sites of saline water with TDS range (39,215–45,220 ppm). The geochemical analysis results show that positive correlation was found between water salinity of the sampling sites and the chemical constituents CaO %, MgO %, K2O %, Na2O %, LOI %, Sr/Ca, and Mg/Ca and the trace elements Co, Ni, Rb, Sr, Zn, Cu, Ba, Cr, and Pb concentrations, while negative correlation was found between water salinity and SiO2, Al2O3, P2O5, and Fe2O3 percentages in the calcite shell of C. cucullata. It is good to use the mineralogical evidence of C. cucullata shells with their living aqueous habitat to build an aqueous environment pollution models. Thus, the shells of C. cucullata were found to be a useful tool for monitoring contamination in the Iraqi aquatic brackish and marine environments.